The Indian seventh seed lost to World No.3 Shixian 17-21, 10-21 in 43 minutes of the Super Series Premier Friday. With this win, the Chinese bettered her head-to-head with Saina to 3-4.
Fourth seed Shixian will next play compatriot and former world champion Yihan Wang in the semi-finals.
This is World No.7 Saina's third quarter-final loss at the prestigious tournament while her previous best performances here were reaching the semi-finals in 2010 and 2013.
Only two Indians -- Prakash Padukone and Pullela Gopichand -- have won this tournament in the past.