After tying at 9-9, Axelsen reinforced his strong smashes to take a 21-15 lead. Chen failed to come back and Axelsen wrapped up the second set 21-12.
In their previous encounter at Rio 2016, Chen routed Axelsen 21-14, 21-15 in the semifinal before he beat Malaysia's legendary shuttler Lee Chong Wei to win his first Olympic gold.
Earlier in the day, Indonesia's fifth seed Anthony Sinisuka Ginting needed only 38 minutes to defeat the tournament's dark horse and world No.59 Kevin Cordon from Guatemala 21-11, 21-13 and won the bronze medal.