Objective To enhance the biodesulfurization rate using a kinetic model that directs the ratio of Dsz enzymes. Results This study established a kinetic model that predicted the optimal ratio of Dsz enzymes in the 4S biodesulfurization system to be A:B:C = 1:2:4 and 1:4:2. When BCAD+1A+4B+2C, the conversion rate of dibenzothiophene (DBT) to 2-hydroxybiphenyl (HBP) was close to 100% in vitro. When the gene dose of dszC was increased, the HBP yield of the recombinant strain BL21(DE3)/BCAD + C reached approximately 0.012 mM in vivo, which was approximately 6-fold higher than that of the BCAD strain. Conclusions According to the results predicted by the enzyme kinetic model, maintaining higher concentrations of DszC and DszB in the desulfurization system can effectively improve the desulfurization efficiency.