For a further understanding of biofilter, a mathematical model is developed based on the analysis of the main effects on the up flow anaerobic biofilter(UFAB), which can characterize not only the substrate removal dynamics but also the gradual biofilter clogging. The model considers three aspects: the biological reaction, deep filtration and hydrodynamics, and consists of flow rate of UFAB, the substrate and suspend solid concentration in the influent, and diameter, surface area, porosity of support medium. By applying the model to the experimental UFAB, and contrasting the simulated and experimental data, the authors prove the model can simulate availably the performance of the biofilter, which is operated on different loading and environment. The model can be used as an effective tool for the wastewater treatment plants operation management and the biofilter optimizing design accurately.