The fourth seeded India, who had reached the finals of 2016 Senior National Championship, recovered from a second game slump to outclass Chong 21-15, 17-21, 21-17 in a 57- minute final.
It was Lakshya's third international title.
In women's singles, M Tanishq staved off a challenge from compatriot Shikha Gautam 17-21, 22-20, 21-18 to clinch the title after battling for an hour and five minutes.
Results:
Men's singles: Lakshya Sen (IND) bt Yee Han Chong (MAS) 21-15, 17-21, 21-17
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Women's singles: M Tanishq (IND) bt Shikha Gautam (IND) 17-21, 22-20, 21-18
Women's doubles: Putri Sari Dewi Citra/Yujia Jin (INA) bt Jee Lynn Lim/Zhen Yap 20-22, 21-9, 21-13
Mixed doubles: Tang Jie Chen/Liu Ying Goh (MAS) bt 8- Rohan Kapoor/Kuhoo Garg 21-19, 21-13.
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