The 16-year-old, airlifted to the city last year for life-saving surgery at the Queen Elizabeth Hospital, now lives with her family in Birmingham.
"This city is the beating heart of England. Birmingham is very special for me, because it was here I found myself alive seven days after I was shot," Malala said at the launch of the new 189-million pound Library of Birmingham.
"This event proves this city loves me and I love it too," she said as she placed her copy of Paulo Coelho's "The Alchemist" on the shelves among millions of books.
Malala also unveiled a commemorative plaque during the ceremony and received her membership card for the archive.
The new building contains the Shakespeare Memorial Room, home to a collection of 43,000 books, including copies of the Bard's First, Second, Third and Fourth Folio editions.
"A fusion of the digital and the traditional is absolutely essential to the vision of the library we have," library director Brian Gambles said in reference to the seven-year project he has led.
Malala was attacked by Taliban fighters on a school bus near her former home in the Swat Valley of northwest Pakistan last October. She was targeted for campaigning for girls' rights to go to school without fear.
She survived the attempt on her life and surgeons later inserted a titanium plate and a cochlear hearing implant.
Malala has since resumed her studies at Edgbaston High School in Birmingham. Her family continues to face threats from the Tehrik-e-Taliban Pakistan.
In July, she was praised for her bravery by UN Secretary-General Ban Ki-moon when she addressed the world body's youth assembly on her birthday.
Malala has since been awarded the Tipperary international peace award and the international children's peace prize. Earlier this year, she signed a deal worth about USD 3 million to publish her story.