The application of livestock and poultry manures to the field as organic fertilizers can maintain and improve soil fertility, which is beneficial to the sustainable development of agriculture. In order to clarify the effects of different manures on soil biological properties, a field experiment was conducted in Ulanqab of Inner Mongolia, including four treatments of chemical fertilizer (F), goat manure (GM), pig manure (PM) and cow manure (CM), soil nutrients, enzyme activities and microbial communities were determined under the different treatments. The results show that, compared with F, application of manures trends to insignificantly increase the contents of soil nutrients such as organic matter, total nitrogen, available phosphorus and ammonium nitrogen. The highest increase rates of soil urease, invertase, alkaline phosphatase and catalase activities under different manures are 32.4%, 150.4%, 26.8% and 30.1%, respectively. Soil microbial biomass carbon and nitrogen under cow manure are significantly increased by 33.2% and 33.4%, respectively. The dominant populations are relatively consistent at the phyla level of bacteria under different treatments, which are Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi and Firmicutes. Under the experimental conditions, different manures have different effects on soil nutrients and enzyme activities, cow manure can improve soil microbial biomass carbon and nitrogen, the short-term application of different manures has no significant effect on the diversity of soil microbial communities, soil pH, available phosphorus, and ammonium nitrogen are the main environmental factors that affect the structure of soil microbial community.