As a natural lagoon, rich in biological resources including fish, crabs, and bivalves, Da-Peng Bay Lagoon receives the discharges from the neighboring rivers, Kao-ping, Dong-gang, and Lin-Bian, which have harmed the ecology and reduced the water quality of the lagoon. This study analyzes seasonal variation of heavy metals concentration (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) in the muscle and viscera of the green-lipped mussel Perna viridis from Da-Peng Bay Lagoon. Data from this study may provide information on the use of Perna viridis as a bioindicator for heavy metals pollution in the lagoon. The heavy metals concentrations were greater in viscera than in muscles of the green-lipped mussel Perna viridis. Results showed that the mussel is capable of accumulating high contents of Cu and Zn. Generally, the order of concentrations in the muscle by season was Zn > Cu > Cr or As. In viscera, the general order of concentrations was Zn > Cu > Pb or Cr or As. Mercury was not detected in winter and spring in muscle and viscera. Cadmium displayed significant variation with season. There was also significant correlation between tissue concentration and heavy metals, including Cu, Pb, Zn, Ni, Cd, and As.