In the women's singles final, Tai Tzu Ying of Chinese Taipei beat Sung Ji Hyun of South Korea 21-17, 21-12.
Chen finishing off the men's singles title match in just 47 minutes against his seventh-ranked opponent from Denmark.
The season-ending tournament was a superb high for the 25-year-old Chinese, who qualified for the competition following victories at the Korea Open and Denmark Open this year.
Chen has now won 18 major titles, including five Super Series Premier, six Super Series and yesterday's second Super Series Finals. In addition, he won the bronze medal at the 2012 London Olympics.
In the women's singles, Tai showed an early resolve as she led 11-3 at the first change-over. Sung tried to use her superior reach and out-fox her shorter opponent. But Tai showed versatility often catching Sung off-guard to take the first set 21-17.
The second set too moved in a similar direction with Tai going in with a 11-5 advantage at the change-over. Tai, who ended runner-up at last year's finale where she went down to China's Li Xuerui eventually eased her way through the set 21-12 to claim her first-ever Superseries Finals crown.
In the men's doubles top-ranked pair of Lee Yong Dae and Yoo Yeon Seong of South Korea fought from a one-set deficit to win 19-21, 21-19, 21-16 against seventh-ranked Chai Biao and Hong Wei of China.
China's Zhao Yunlei shrugged off her earlier disappointment of losing in the women's doubles to pick up the mixed doubles title by partnering Zhang Nan for a 21-15, 21-12 win over team-mates Liu Cheng and Bao Yixin.
Misaki Matsutomo and Ayaka Takahashi of Japan beat Tian Qing and Zhao Yunlei of China 21-17, 21-14 for the women's doubles.
Men's Doubles: Lee Yong Dae/Yoo Yeon Seong (South Korea) bt Chai Biao/Hong Wei (China) 19-21, 21-19, 21-16.
Women's Doubles: Misaki Matsutomo/Ayaka Takahashi (Japan) bt Tian Qing/Zhao Yunlei (China) 21-17, 21-14.
Men's Singles: Chen Long (China) bt Hans-Kristian Vittinghus (Denmark) 21-16, 21-10.
Women's Singles: Tai Tzu Ying (Chinese Taipei) bt Sung Ji Hyun (South Korea) 21-17, 21-12.
Mixed Doubles: Zhang Nan/Zhao Yunlei (China) bt Liu Cheng/Bao Yixin (China) 21-15, 21-12.