The freshwater polyculture pond culturing occupied an important position in the aquaculture industry. Accumulation of trace metals was investigated in water, sediments, and fish (Carassius auratus, Cyprinus carpio, Ctenopharyngodon idellus) from typical polyculture ponds in Chengdu, China. The results showed most of the pond water in Chengdu were safe for fish cultivation. The Cd and Cr concentrations in sediment samples from sites S3, S4, and S9 which were near the industrial park and road with a high traffic volume were higher than those of the other sites. Cu, Cr, Fe, Zn, Mn, Ni, and Pb in sediments were unpolluted, while Cd was unpolluted to moderately polluted due to anthropogenic activities. Cu, Cd, and Pb in fish pond sediment of Chengdu had higher potential mobility under normal environmental circumstances. The trace metal concentrations in liver of three fish species were all higher than those in muscle tissues. The order of bioaccumulation factor (BAF) values for trace metals was Cr > Cu > Pb > Zn > Cd > Ni > 20. The concentrations of Cu, Cd, Pb, Zn, and Cr in the muscle of three fish species were all below the local and international maximum permissible levels. The target hazard quotient (THQ) and hazard index (HI) of trace metals in aquaculture fish ponds in Chengdu were lower than 1, which indicated that the consumption of grass, crucian, and common carp cultivated in the aquaculture ponds of Chengdu pose no health risk to the residents.