Soil microorganisms play a crucial role in maintaining soil ecosystem health. Their metabolic processes are directly impacted by various environmental stresses caused by the increasing release of chemical pollutants and changes in the physical environment due to rapid societal development. This paper aimed to investigate the mechanisms underlying the changes in soil microbial stress responses under various external environmental stresses. The impact of pollutants on soil ecological structure was analyzed by summarizing the stress response patterns of soil microorganisms to inorganic pollutants, organic pollutants, and extreme physical environmental factors. Additionally, the migration and transformation behaviors of various complex pollutants, facilitated by the involvement of soil microorganisms, were investigated. Moreover, a novel approach was proposed for pollutant control, suggesting that manipulating the external physical field of a certain intensity could guide microbial communities and their functions towards controllable evolution within the soil environment. Therefore, this paper was essential for exploring the diversity of soil microbial stress responses, strategically regulating contaminant transport, mitigating risks associated with soil complexity, and ultimately reshaping soil ecological functions.