Whether genetic factors affect social cognition, particularly emotion management, requires elucidation. This study investigates whether social cognition varies with genetic variations of COMT and tryptophan hydroxylase-2 (TPH2), which modulate dopamine and serotonin neurotransmissions respectively, and thereby emotion regulation. NIMH-recommended "managing emotions branch and 2 subtasks" of MSCEIT and six neurocognition domains, and genotypes of COMT Val158Met and TPH2 G703T were measured in 150 Han-Chinese healthy adults. Subjects carrying the M allele (M group) of COMT exceeded Val/Val homozygotes (V group) in managing emotions branch (p = 0.032) and emotional relation subtask (p = 0.037). TPH2 T/T homozygotes (T group) excelled those with the G allele (G group) in emotional management subtask (p = 0.025). Subjects with M+T variation surpassed the other 3 groups (M+G, V+T and V+G) in managing emotion branch (p = 0.002), emotional relation subtask (p = 0.023), and emotional management subtask (p = 0.002). The findings remained after control for gender, age, education, and neurocognitive functions. Synergistically, the effect size of COMT-TPH2 combination surmounted the sum of separate effect sizes of COMT and TPH2. The findings suggest that genetic variations of COMT and TPH2 have synergistic effects on social cognition in the general population.