The current study investigated the toxic effects of Cu2+, Zn2 , and Pb2 on the embryos and larvae of Epinephelus septemfasciatus. The results indicated that as the three heavy metals ion levels increased the fertilized egg hatching speed and the hatching rate gradually declined while the malformation rate gradually increased. The malformation of the embryos and larvae included bended tail sprouts, incomplete hatching, the “L”, “S” and “V”-shaped vertebrate of newly-hatched larvae and comma-shaped un-expanded tail deformity. Based on the comprehensive hatching rate, hatching rate and malformation rate, the toxicity to the embryonic development of these heavy metal ions were: Cu2 > Zn2 > Pb2 . The newly-hatched larvae toxicity test cycle was 96 h. The survival rate of the larvae gradually reduced with the increased time. The increased concentrations of these heavy metal ions dramatically decreased the survival rate while increased the number of deformity. Based on the time period of the half lethal concentration (LC50) and the safety concentration, the toxicity of three heavy metal ions on the newly-hatched larvae were: Cu2 > Pb2 > Zn2 . These results may contribute to the formulation of new fishery water quality standard and parameters of water environment monitoring and provide important scientific basis for E. septemfasciatus breeding of heavy metal monitoring and management.