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The phrase it is the thought that counts, and its variants, mean: the value to the recipient of a gift lies in the goodwill or affection with which the gift is given.

These are, in chronological order, the earliest occurrences of this phrase that I have found:
—Note: With one exception, all these quotations refer to the Christmas season:

1-: From As to Christmas Giving, by ‘A Lady in a Toledo Paper’, published in The Iowa State Register (Des Moines, Iowa, USA) of Sunday 20^th December 1885 [page 9, column 2]:

It seems to me that there is something very beautiful in this custom of putting heart thoughts in some little gift, that all over the land each one is trying to give pleasure to others, to make life a little brighter by these tokens of friendly regard. Even if it has been done at a little self-sacrifice, it is well, for the very effort has driven self in the background, and made the world a brighter place for somebody to live in. There is one thing, however, to be kept in mind, and in a forgetfulness of this lies the trouble. It is not the value of what is given that is to be considered. It is the friendly thought which counts. Never, therefore, be betrayed into the folly of giving what you cannot afford, because you may think it is expected, or you imagine the recipient has so much that a simple thing will be uncared for.

—Note: The above-quoted text was reprinted in several newspapers. The Oxford English Dictionary (online edition, 2025) mistakenly states that The Spirit Lake Beacon (Spirit Lake, Iowa, USA) published it on Thursday 1^st January 1885, while, in fact, it published it on Friday 1^st January 1886 [page 1, column 4]—it is true, however, that the frontpage was erroneously dated Friday 1^st January 1885.

2-: From Sending the Christmas Box to Manila, a short story by Alice Rix, published in The San Francisco Call (San Francisco, California, USA) of Sunday 20^th November 1898 [page 17, column 6]:

“Do they take papers?” asked an old man in an army coat.
“Take anything,” said a man running by with a truck.
“Where can I leave this?” asked the old man, looking around. But the man with the truck was gone.
“I’ll take them up for you,” said a fresh-faced girl, stretching out her hand.
“Thank you,” he said, putting the papers into it. “They’re not much to send but I wanted to send something and wouldn’t like to have them overlooked——”
The girl flushed a little. “I’m sending papers, too,” she said.
The old man looked at her with gentle eyes.
“It’s the thought that counts, my dear,” he said softly.
“Yes,” said the girl, smiling up at him, “I know.”

3-: From an advertisement for Dives, Pomeroy & Stewart’s, published in the Harrisburg Telegraph (Harrisburg, Pennsylvania, USA) of Wednesday 21^st December 1898 [page 8, columns 1 to 5]:

Store Open Every Evening Until 10 O’clock Up to Christmas.

The Real Joy of the CHRISTMAS TIDE.

It is found—after all—in giving—not getting. Don’t you agree with me? Or are you a pessimist, always looking on life through blue glasses?
If you are, come to Dives, Pomeroy & Stewart’s. Watch the throngs, filled with the true Christmas spirit—fathers, mothers, big sisters and brothers—all intent on making some one happy. No self seeking here. Even though the gift be small in value, what matter that? It is the thought that counts.
Use the new entrance on Fourth Street and add to your comfort.

4-: From How to Treat Your Wife, by ‘One Who Knows’, published in The Toowoomba Chronicle, and Darling Downs General Advertiser (Toowoomba, Queensland, Australia) of Saturday 11^th August 1900 [page 7, column 1]:

A bunch of flowers for the table, or a posy of violets to wear, will please her. She misses the buttonholes you gave her when you were courting, and she is too honorable to buy them for herself out of the house keeping money. I don’t mean you should ruin yourself at an expensive florist’s. A couple of rosebuds or a homely bunch of pansies will give her more delight than costly hothouse blooms. It’s the thought that counts. A man I know brings his wife a buttonhole every Saturday night for Sunday; once when he was where he couldn’t buy any for love or money, he gathered her a bunch of buttercups, and she wore them as proudly as if they had been orchids. The cost of the gift is less than nothing, the love which prompts it is all that matters.

5-: From The Ladies Page, by ‘Magpie’, published in The Adelaide Observer (Adelaide, South Australia, Australia) of Saturday 24^th November 1900 [page 39, column 4]:

This week was the Christmas mail for England.
“Did you remember?” I asked “That Girl.”
[…]
“I wrote,” she said, “but it was hard. […]”
[…]
And then we shall have to think of the nearer folks—to make our lists like the small person who broke into song.
Wearisome—a matter of form—mere duty giving?
That is as you choose. To those who have given, it is only graceful to give in return, but besides there are others. Look through your list and mark the names of whose [sic] who will not have much of a Christmas for special thought. Give useful things, by all means, but also some touch of the beautiful to make a festival of it. Choose suitably with due consideration of tastes and hobbies.
Takes time and thought?
Of course it does. That is when the real giving comes in.
“Of course, the mere thought counts,” said That Girl, “but people do make strange mistakes—their thoughts run so to fancy things. Do you remember that hit in ‘The Autocrat,’ when the well-to-do relations sent the poor lady an expensive bouquet, and the landlady’s rich uncle sent her a plaster of paris [sic] Venus, which she promptly rolled up in a towel and hid?”