Accurately modeling and predicting the migration and degradation of contaminants in unsaturated soil have fatal research significance for pollution controlling, environmental protection and ecological restoration. However, most of the current numerical models either simplify the microbial degradation process to a zero-or first-order degradation process and decrease the modeling accuracy, or focus on describing one kind of microbial degradation process and cannot be used as an universal way. To make the numerical model with high modeling efficiency and universal applicability, microbial degradation module, incorporating the effects of microbe propagation, is coupled into the traditional water flow, heat transfer and solute transport model in this research. The migration and degradation of contaminants in solid phase, liquid phase and gaseous phase, sequential decay processes, and degradation under the interaction of multiple microbes are intergraded into the new model. Besides, the effects of microbe propagation and multiple inhibition factors on contaminant degradation are considered in the new model. Furthermore, the zero-and first-order degradation processes in the traditional model are also kept in the new model. Thus, the new model is with both good practicality and applicability. The modeling comparison illustrates that the bio-degradation in unsaturated soil affects solutes transport and can not be ignored.