In order to improve the spatial resolution of the imaging system, the influence mechanisms of the focal spot size and envelope shape in the focused refractive index microscopy imaging system on the spatial resolution are analyzed, and a method for improving the imaging spatial resolution through a numerical deconvolution algorithm is proposed. First, the spatial field distribution of the focused generalized cylindrical vector beam is analyzed, and then the difference between the influence of this beam and the ideal slim beam on the spatial resolution during the refractive index microscopic imaging process is compared. By measuring PS (Polystyrene) spheres with known refractive index and shape, the point spread function of the system under the experimental conditions is obtained. The deconvolution algorithm is used to reconstruct other sample images to obtain experimental results closer to the real situation. The results show that this method has a significant effect on improving the imaging quality and spatial resolution of the system.