The exhaust gas of marine diesel engine under rated condition is taken as the research object, the newer version of fluent18.0 software is used as the platform, the self-defined function and SO2 absorption model are compiled by using C++software and double membrane theory, and the compiled self-defined function is imported through UDF interface. The uneven distribution of flue gas and the phenomenon of sticking to the wall in the side feed desulfurization tower lead to the reduction of desulfurization efficiency. The number and position of the guide plates in the flue of the marine desulfurization tower need not be simulated and optimized. Through the analysis and comparison of the velocity flow field and SO2 mass fraction cloud chart, the desulfurization efficiency of zero to three guide plates is 94.31%, 95%, 96.84% and 97.63% respectively. Then, compared with the experimental data, and the difference of simulation results is small, which has great practical value and theoretical significance for optimizing desulfurization tower and improving sodium alkali desulfurization system.