Despite our extensive knowledge on the effects of long-term straw returning on soil, little is known about the effects of short-term straw returning. We identified three study sites and evaluated their soil organic matter (OM), pH, and enzyme activity after two years of straw returning treatment. Bacterial diversity and community were determined by 16s RNA sequencing. We observed elevated OM content and pH after short-term straw returning treatment. The bacterial phyla Proteobacteria and Bacteroidetes exhibited similar dynamics on straw application. We observed reduced levels of Actinobacteria and Chloroflexi bacterial phyla after straw returning. Reduced Actinobacteria and Chloroflexi may be due to competition from dominant bacteria. In general, OM content and enzyme activity had the same trend that closely correlated with the amount and community of microorganisms in the soil. Proteobacteria and Bacteroidetes were the critical phyla in straw degradation and might improve soil OM content. Proteobacteria and Actinobacteria were identified as copiotrophic taxa. In summary, straw returning treatment might maintain soil stability and bacterial diversity better. The bacterial phyla Proteobacteria and Bacteroidetes were dominant over other microbial fractions during straw decomposition. The survival competition might be one of the main reasons for the decrease of Actinobacteria and Chloroflexi. Short-term straw returning to the field can markedly improve soil quality. However, soils in different locations respond differently to straw return practices and their responses are influenced by the soil’s basic parameters and climate.