The fourth seeded Indian, 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.
In the men's doubles, World No 2 Kidambi Srikanth's brother Kidambi Nandagopal and his partner Alwin Francis went down 21-19, 21-15 to Arun George and Sanyam Shukla.
Results: Men's: Singles: Lakshya Sen (Ind) bt Yee Han Chong (Mas) 21-15, 17-21, 21-17
Doubles: Arun George/Sanyam Shukla (Ind) bt Alwin Francis/K Nandagopal (Ind) 21-19, 21-15
Women's: Singles: M Tanishq (Ind) bt Shikha Gautam (Ind) 17-21, 22-20, 21-18
Doubles: Putri Sari Dewi Citra/Yujia Jin (Ina) bt Jee Lynn Lim/Zhen Yap (Mas) 20-22, 21-9, 21-13
Mixed doubles: Tang Jie Chen/Liu Ying Goh (Mas) bt 8-Rohan Kapoor/Kuhoo Garg (Ind) 21-19, 21-13.
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