Veteran batsman Steve Smith dropped from the team
His victory, which took 65 minutes, sets up a final against another Chinese player, Chen Long.
Five-time world champion Lin allowed Shi to dictate the pace at the start of the opening game before seizing back the initiative, and winning 21-19.
A couple of unforced errors paved the way for Shi to level with a 16-21 win in the second game, but Lin came to life in the decider and clinched the match.
It is the second final that Lin has reached this year but the two-time Olympic gold medallist conceded it was tough to battle past Shi.
"Nowadays the competition within the Chinese men's singles team is as strong as against others. But I am used to the pressure, and the most important thing is to be consistent," Lin said
Lin will play Chen in a repeat of the 2015 final, which was won by Chen.
Chen was equally impressive in his 64-minute victory over Jonatan Christie of Indonesia, pulling out some powerful forehand smashes to win 12-21, 21-10, 21-15.
The women's singles saw Taiwanese Tai Tzu-ying set up a final clash against Japan's Akane Yamaguchi.
Tai was impressive in her 21-14, 21-19 win over China's Chen Yufei, while Yamaguchi was equally impressive in her victory over compatriot Nozomi Okuhara, winning 21-15, 22-20.
Results (x denotes seeding)
Men's singles
Lin Dan (CHN) bt Shi Yuqi (CHNx2) 21-19, 16-21, 21-12
Chen Long (CHNx4) bt Jonatan Christie (INA) 12-21, 21-10, 21-15
Women's Singles
Tai Tzu-ying (TPEx1) bt Chen Yufei (CHNX3) 21-14, 21-19
Akane Yamaguchi (JPNx4) bt Nozomi Okuhara (JPNx2) 21-15, 22-20
Men's Doubles
Takeshi Kamura-Keigo Sonoda (JPNx3) bt Fajar Alfian-Muhammad Rian Ardianto (INAx8) 21-13, 22-20
Li Junhui-Liu Yuchen (CHNx2) bt Takuro Hoki-Yugo Kobayashi (JPN) 13-21, 21-19, 21-15
Women's Doubles
Du Yue-Li Yinhui (CHN) bt Jongkolphan Kititharakul-Rawinda Prajongjai (THAx8) 21-12, 21-14
Chen Qingchen-Jia Yifan (CHNx5) bt Chang Ye-na-Jung Kyung-eun (KOR) 21-14, 21-18
Mixed Doubles
Zheng Siwei-Huang Yaqiong (CHNx1) bt Dechapol Puavaranukroh-Sapsiree Taerattanachai(THAx4) 21-14, 21-9
Wang Yilyu-Huang Dongping (CHNx2) bt Tan Kian Meng-Lai Pei Jing (MAS) 21-13, 21-17
Veteran batsman Steve Smith dropped from the team
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