A comprehensive mathematical model was developed to describe the cometabolic biotransformation of chlorinated solvents at enzymatic level. The major factors considered in modeling included not only the utilization of primary substrate, the cometabolic degradation of chlorinated solvents and microbial growth, but also the induction of key enzymes, toxic inactivation, self‐recovery and the role of energy. Model simulation was conducted in a batch system for trichloroethylene (TCE) degradation by methanotrophs, with methane as primary substrate and formate as exogenous energy source. Model parameters were obtained from published literature. Simulation results indicated that the primary substrate donominated the key enzyme production, energy supply and microbial growth. TCE cometabolism resulted in the activity loss of key enzymes and the consumption of energy in terms of reducing power. The function of self‐recovery was able to offset the impact of the toxic inactivation to some extents. Formate as energy substrate can stimulate TCE biodegradation by supplying extra reducing power. The results were compared with the phenomena reported in literature.