Antibiotics act as an ecological factor in the environment that could potentially affect microbial communities. The effects include phylogenetic structure alteration, resistance expansion, and ecological function disturbance in the micro-ecosystem. Numerous studies have detected changes of microbial community structure upon addition of antibiotics in soil and water environment. However, the causal relationship between antibiotic input and resistance expansion is still under debate, with evidence either supporting or declining the contribution of antibiotics on alteration of antibiotic resistance. Effects of antibiotics on ecological functions have also been discovered, including nitrogen transformation, methanogenesis, and sulfate reduction. In the latter part, this review discusses in detail on factors that influence antibiotic effects on microbial communities in soil and aquatic environment, including concentration of antibiotics, exposure time, added substrates, as well as combined effects of multiple antibiotics. In all, recent research progress offer an outline of effects of antibiotics in the natural environment. However, questions raised in this review need further investigation in order to provide a comprehensive risk assessment on the consequence of anthropogenic antibiotic input.