The process of urbanization transforms natural ecosystems to anthropogenic urban landscapes dominated by impervious surfaces. Such landscape transformation alters both the survival environment and spatio-temporal heterogeneity of airborne microbial communities. The impact of urbanization on airborne microbial communities contributes to regulate the ecological functions of microbial communities. The transformation of microbe communities resulting from urbanization might also reduce environmental quality and create a threat to public health. The spatial and temporal scales of these two environmental processes noticeably differ (urbanization process and dynamic of microbial communities). The coupling of these two macro- and micro-processes is receiving the increasing focus in the research field of ecological security and environmental health. This study presents a systematic review of studies on airborne microbial communities in the urban environment. The sources and community characteristics, spatio-temporal heterogeneity and affecting factors, and eco-environmental effects of airborne microbial communities were explored. The limitations of current studies on this topic were examined from a macroecological perspective. We suggest that theories of social-economic-natural eco systems and landscape patterns and processes should be introduced to identify the relationships between urbanization and the dynamics of airborne microbial communities and their potential impacts on public health. In conclusion, this review provides insights to improve the living environment during the rapid urbanization process.