The world No 1 was beaten by the two-time All England champion and fifth seed 15-21, 13-21 in 41 minutes.
It was Saina's sixth defeat to the Chinese in 12 meetings.
The Indian ace grabbed a slender 4-2 lead in the first game, but Shixian soon took control and went into the break 11-8 ahead.
Saina fought back and drew abreast at 14 but Shixian reeled off six straight points, allowing the Indian just one, before wrapping the game.
In the second, the Chinese continued to call the shots and led 6-3. Though Saina made it 6-all and then 10-all, Shixian proved too strong as she raced away from 13 to seal the game and match.
Saina’s next tournament is the Indonesia Open Super Series Premier tournament, starting June 2.
Image: Saina Nehwal
Photograph: PTI