The 31-year-old actress says it's a major compliment and that she never dreamed of such a thing.
Nyong'o took Hollywood by storm this year, winning a best supporting actress Oscar for her performance in "12 Years a Slave."
While growing up in Kenya, the actress says she equated beauty with what she saw on television, believing that beauty was "light skin and long flowing straight hair."
In an interview, she said she'd never dreamed she'd be called beautiful because she didn't like the way she looked as a teenager.
Nyong'o said her mother always said she was beautiful, and that she finally she believed her at some point.
The actress hopes this will show other teenagers and women of all ages to accept the way they look, noting that her selection for this year's cover made her, "happy for all the girls who would see me on it and feel a little more seen."
(The Associated Press contributed to this report)
