Abstract: Groundwater contamination is a global environmental issue that seriously threatens human health and ecological environment. As an essential component of groundwater ecosystems, microorganisms are involved in a series of biogeochemical processes through their metabolic reactions, which control the transformation and transport of contaminants. Numerical simulation of the contaminants transport and transformation is an effective method to quantitatively describe and predict their behaviors. Understanding and handling the modeling of microbial metabolic processes can significantly improve the accuracy of simulation and prediction of contaminants behaviors in groundwater. Here, this review systematically summarizes the development process of microbial metabolic activities according to the development timeline and application scales, focusing on the advancement of next-generation gene sequencing technology to promote numerical simulation research. Meanwhile, this review analyzes how to construct microbial metabolism models to quantitatively describe the biogeochemical processes they are involved in, and summarizes the commonly used microbial information databases and simulation software. It is pointed out that the current application of microbial metabolism modeling still faces many challenges, including verification difficulty, low parameter applicability, data acquisition difficulty, and high computational demands. Future research should further explore microbial metabolic mechanisms, optimize microbial metabolic modeling methods, and improve parameters and empirical equations under different demands, to enhance the accuracy and applicability of models, as well as to solve the issues of microbial-related data processing and computational precision and efficiency in model establishment.