The distribution and risk assessment of heavy metals (Pb, Cu, Cr, Zn, Cd, As and Hg) in the economic fish of the Southern Fujian Province was acquired. The Cd content was below the detection limit. 53.5% of As and 26.7% of Hg were lightly polluted, but the indices of Pin (Nemero comprehensive pollution index) and MPI (metal pollution index) both indicated no pollution. The indices of EDI (estimated daily intake) and THQ (target hazard quotient) both indicated no non-carcinogenic risk of HMs. The index of Ri (average annual cancer risk) verified no carcinogenic risk for Pb and acceptable risk for As. Furthermore, molecular docking results revealed As may have significant reproductive toxicity to humans. Our findings serve to heighten an awareness of economic fish consumption and provide a reference for marine environmental management and food security in study area.