The third seeded Indian eked out a 21-11 18-21 21-17 win over Sun in a quarterfinal battle that lasted an hour and 11 minutes at the Putra Stadium here.
The girl from Hyderabad will next take on Olympic champion Li Xuerui, who had withdrawn from the BWF World Super series last year due to an injury and also skipped India Super Series last week.
The two-time World Championship silver medallist has defeated Saina eight times, while the Indian beat her twice -- once during the 2010 Singapore Open and then at 2012 Indonesia Open.
Brimming with confidence after her India Open triumph and ascent to World No.1, Saina zoomed ahead to 12-4 with a eight-point burst and never looked back. He grabbed the first game rather comfortably.
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The World No. 15 Sun, however, made a flying start in the second game, opening up a 7-1 lead early on but Saina soon caught up with the Chinese at 14-14. Sun then slowly started to distance herself from the Indian and made a successful return to the match.
Saina has been on a roll ever since winning the China Open last year. She clinched the Syed Modi Grand Prix Gold, reached the finals of All England Championship, before winning the India Super Series last week.