Pollution of arable land caused by heavy metals in livestock and poultry manure has become a potential threaten to human health in China. Safe disposal of the contained toxic pollution with animal manure by co-composting with biochar is one of the alternative methods. Biochars from different sources (wheat straw, peanut shells and rice husks) amended with different loading rates were investigated for passivations of copper and zinc (Cu and Zn) in swine manure composting. Results showed that the passivation effects of the three types of biochar on Cu and Zn were enhanced with increasing biochar dose. Contents of Cu and Zn measured by diethylenetriaminepentaacetic acid (DTPA) and Community Bureau of Reference (CBR) showed that wheat straw biochar with the loading rates of 10％–13％ (w/w) was superior to the other two types of biochar in this study. Compared with the control, sample from wheat straw biochar was more favorable for the bacterial growth of Proteobacteria, Firmicutes and Actinobacteria. In addition, pot experiment showed that organic fertilizer amended with wheat straw biochar could significantly improve the growth of Chinese pakchoi and enzyme activities (superoxide dismutase, peroxidase, polyphenol oxidase and catalase) as compared with the control. Cu and Zn contents of Chinese pakchoi in the organic fertilizer group containing wheat straw biochar reduced by 73.2％ and 45.2％, 65.8％ and 33.6％, respectively, compared with the group without loading biochar. There was no significant difference in the contents of vitamin C and reducing sugar between the groups of organic fertilizer amended with/without wheat straw biochar, however, there was significant difference compared with the heavy metal addition group. The application of organic fertilizer formed by adding biochar can effectively reduce the adverse effects of heavy metals on crops.