Biogas residue (BR) is widely used as a new green fertilizer in agriculture in China. However, it often contains a high concentration of heavy metals so its application should cause our concern. An incubation experiment was conducted to study the risk of pig biogas residue (PBR) and chicken biogas residue (CBR) application on Liuminying soil (LS) and Yixing soil (YS). The soils were incubated for one, three and six months with 0, 2%, 4% and 6% addition of BRs. According to BCR extraction results, the PBR and CBR applications induced an increase in the concentration of exchangeable fraction of Zn. As for the concentration of exchangeable fraction of Cu, an increase was only observed in the treatments with PBR application. The heavy metal binding intensity also showed a similar trend. With the PBR application, for the LS and YS, the highest concentrations of exchangeable Zn increased 3.6 and 9.5 times, respectively, while the exchangeable Cu was increased by 52.6% and 187.1%. Dissolved organic carbon was the limiting factor for the exchangeable Cu while the exchangeable Zn was controlled by soil pH. PBR presented more agricultural risk than CBR when used as fertilizer. Meanwhile, BRs were more adaptable to LS than YS according to the heavy metal release results.