Having made a quarterfinal exit at the World Cup Stage I in Shanghai, the former world number one put up a consistent display with 34 perfect 10s to total 672, five points ahead of Taipei's Peng Chia-Mao to bag the topseed as she will begin her campaign from the last-32.
Deepika's teammates Monika Saren and Preeti finished 31st and 45th respectively as the team ranked fifth in the draw of 16.
In the men's recurve category, Dhaniram Basumatary was the best placed Indian at seventh with 667, two points ahead of Olympian Atanu Das who finished 13th.