This study explored the effects of combined application of biochar and cow (N), sheep (Y) and pig (Z) manures in different proportions. The field experiment was carried out in Xiuzhou District of Jiaxing City, soil physicochemical properties, enzyme activity and bacterial community structure were determined and compared. The results showed that the treatments of biochar with manure increased soil pH and organic matter content by 4.34%-16.24% and 18.70%-46.28%, respectively, compared with CK (no biochar and manure), and also significantly increased the contents of soil total nitrogen, alkali hydrolyzable nitrogen and available phosphorus, among of which, N50 (50% cow manure and 50% biochar), Y25 (75% sheep manure and 25% biochar) and Z50 (50% pig manure and 50% biochar) treatments had better effects. Different treatments had different effects on soil enzyme activity, generally, Y25 had the best effect on improving soil enzyme activity. Biochar with manures increased soil bacterial diversity, among of which, N50 significantly increased soil microbial diversity and changed soil bacterial communities, and the bacterial communities under N50, Y25 and Z50 were the most different from CK. Soil pH and total nitrogen were the main environmental factors affecting the variation of bacterial community structure. In conclusion, N50, Y25 and Z50 are recommended to be used in facility soil due to their better effects in improving soil quality.