In this study, the case of super typhoon Lekima, which landed in Jiangsu and Zhejiang Province on 4 August 2019, is numerically simulated. Based on the Weather Research and Forecasting (WRF) model, the sensitivity experiments are carried out with different combinations of physical parameterization schemes. The results show that microphysical schemes have obvious impacts on the simulation of the typhoon’s track, while the intensity of the simulated typhoon is more sensitive to surface physical schemes. Based on the results of the typhoon’s track and intensity simulation, one parameterization scheme was further selected to provide the background field for the following data assimilation experiments. Using the three-dimensional variational (3DVar) data assimilation method, the Microwave Humidity Sounder-2 (MWHS-2) radiance data onboard the Fengyun-3D satellite (FY-3D) were assimilated for this case. It was found that the assimilation of the FY-3D MWHS-2 radiance data was able to optimize the initial field of the numerical model in terms of the model variables, especially for the humidity. Finally, by the inspection of the typhoon’s track and intensity forecast, it was found that the assimilation of FY-3D MWHS-2 radiance data improved the skill of the prediction for both the typhoon’s track and intensity.