In this paper, an enhanced polarization-independent two-layer five-port grating with covering layer is proposed. The rigorous coupled-wave analysis (RCWA) is used to predict grating parameters. In addition, the total efficiency of the polarization-independent five-port grating with covering layer can exceed 80% with the good uniformity of 1.97% for TE and TM polarization. The inherent coupling mechanism and the electric field energy distribution of the gratings are explained well under TE and TM polarization by the simplified mode method (SMM) and the finite element method (FEM). According to the reported five-port gratings, the proposed transmission five-port grating with a covering layer has good uniformity for TE and TM polarization. Moreover, the grating can be protected and the groove of the grating can be kept clean by adding a covering layer during the actual fabrication. At the same time, the fabrication errors of the two-layer five-port diffraction grating are further considered. Therefore, the numerically simulated five-port grating with covering layer has a wide application prospect in precision displacement measurement and holographic projection imaging.