Schulz's letters to his mistress have created controversy among the late cartoonist's family who has called his mistress "indecent" for selling them, said the Daily Mail.
Tracey Claudius is selling the letters, which are expected to fetch up to $350,000.
In an interview with the Mail, Schulz's daughter Amy said that 67-year-old Claudius was "immature" and that her actions were in "bad taste."
At the time of their affair, Claudius was 23 years younger than Schulz-he 48 and she 25.
They met in 1970 while she accompanied her friend during an interview with Schulz, pretending she was a photographer to meet the famous cartoonist.
There are 44 letters with a total of 56 pages and 22 original drawings, which Sotheby's said was the most ever to come to auction by Schulz.
The Associated Press said the letters were often rather light-hearted with Schulz addressing her "Tracey Tracey Tracey" and another saying that she was "beepable," "huggable" and "buggable"-words he used in his cartoons.
The news service also reported that he once sent a dust jacket of a dictionary on which he wrote, "I'm going to return my new dictionary ... there are no words to tell you how much I love you."
She apparently turned down his request to marry her on several occasions.
The auction will take place on Friday, Dec. 14 at Sotheby's.
Schulz died in his sleep in 2000 at the age of 77.