Though fertilizers can improve grain yield, the trace heavy metals in fertilizers will also enter soil and migrate through food chains, which harbor ecological and health risks. This study was based on more than 30 years of location experiments. The objective was to investigate the effects of different fertilizer treatments on the bioavailability of heavy metals in Shajiang black soil. Total and available contents of Cu, Zn, Pb, and Cd in soil samples were determined by atomic absorption spectrophotometry (AAS), and were compared between different treatments by using single factor analysis of variance and least significant difference. Finally the bioavailability indices (BAIs) of heavy metals were calculated. The results show that after treatments of fertilizers, total contents of Cd, Cu, Pb, and Zn increased, but were all lower than China’s Soil Environment Quality Standards (SEQS, level II). Available Cu content was the highest after M treatment; available Zn contents were relatively low after all treatments; available Pb and available Cd contents were the highest after NP treatment. Under different treatments, the BAIs of each heavy metal were largely different. Bioavailability of a heavy metal was affected by soil properties and by its adsorption, desorption, complexation, precipitation, and dissolution in soil. The mean BAI of each metal ranked in the order of Cd > Pb > Cu > Zn; the available Cd and Pb were highly migratory, and thus can be absorbed and enriched by plants, and may finally threaten human health through food chains.