Roger Carlson, whose charming Evanston bookstore was featured as a setting in the novel “The Time Traveler’s Wife,” has died.

Mr. Carlson, 89, the longtime owner of Bookman’s Alley, died of heart failure Friday at his Deerfield home, according to his wife Deborah.

Bookman’s Alley, like “The Time Traveler’s Wife,” had an air of magic. Customers had to walk down an alley to enter the rambling little carriage house filled not just with used books but also posters and antiques and comfy chairs and couches.

Clare, the lead character in Audrey Niffenegger’s novel, observed “the weird little objects that are tucked into the various sections: a saddle in Westerns, a deerstalker’s cap in Mysteries. . . . I begin to peruse the shelves dreamily, inhaling the deep dusty smell of paper, glue, old carpets and wood.”

“I’ve always loved and bought books,” Mr. Carlson once told the Sun-Times. “I’ve deliberately tried to create the atmosphere we have here.”

A Minnesota native, he opened the bookstore off Sherman Avenue in 1979 after working in ad sales in Chicago with National Geographic, Fortune and Parade magazines.

“He hated every minute of it,” his wife said of his earlier career. “He loved books, and he was never a businessman.”

Mr. Carlson operated Bookman’s Alley for 33 years, until declining health prompted him to close in 2013.

Niffenegger started visiting his shop while in high school. “It was a delightful home for book lovers,” she said in an email, “and Roger presided over it with warmth and gentle approval. He might suggest books, or beam at you when you selected something he liked or thought you should read. Bookman’s Alley was like a portal into an older age of book selling. . . .I got an education from Roger and his shop.”

“The funny thing is that after the Harry Potter books came along — and especially the Harry Potter movies — everybody started referring to what Roger had going on here as ‘Harry Potter-esque,’ ” said Nina Barrett, who owns Bookends & Beginnings, the bookstore that opened in Bookman’s Alley’s old space in 2014. “You really had this sense of entering one of these wizard shops, and he was the wizard. And, yes, it was magical — the antiques and the rugs, and you never knew what you were going to find, and what he was going to say to you.”

Despite the seeming disarray, “It was all in his head, and he knew exactly where it was,” said Ross Martens, co-owner of the adjacent Alley Gallery. When Mr. Carlson was hospitalized, “He had a whole army of volunteers that just loved the shop so much they came and ran it while he was away.”

One of his customers was Vivian Maier, the eccentric nanny who gained posthumous fame as a photographer for preserving a bygone Chicago in the street scenes she shot.

“Roger gave her money,” his wife said. “I remember him saying to me that he took her home to where she was living. . . . He said she had newspapers practically up to the ceiling. He said she just left this narrow pathway to get through.”

Mr. Carlson once told Chicago Sun-Times columnist Neil Steinberg he rarely had seller’s remorse, but he did regret having let go of a book by Willard Schultz.

“It wasn’t especially valuable, but the inscription was so great,” he said. “He was a white man who was raised by the Indians in Montana, I think. This was a book published in the ’20s, and his inscription was, ‘So few of us left who lived upon the buffalo.’ I thought that was a very sad inscription.”

Deborah Carlson was a flight attendant for American Airlines when she met her future husband at a popular Chicago bar called Easy Street. He’d served in the U.S. Army and attended the University of Minnesota.

“Mr. Charm,” she said of how he came across. “Sense of humor. Oh, he was handsome. He was tall.”

They got married in 1956.

Mr. Carlson didn’t want a funeral service, she said. He was cremated.

He also leaves behind his daughters Ann Miller, Leslie Carlson-Magee and Susan Carlson, sons Jeffrey and Gregory, 10 grandchildren, three great-grandchildren — and thousands of books that fill much, but not all, of the couple’s home.

“I have one room,” his wife said, “and I wouldn’t let him put any books in it.”