The microstructure distribution on the bottom surface of the partial integrated light guide plate (PILGP) is the key to affecting the uniformity of the output light from the backlight module (BLM), which is one of the important factors in the BLM design. Based on the development trend of the BLM in light-weight and integration, many research institutes have realized the requirement for high luminance and luminance uniformity in the BLM by setting micro-prism structure on the surface of the light guide plate (LGP). In most of these studies, the length of the micro-prism structure is the same as the width of the LGP, and the optimization of the micro-prism distribution is performed only in the length direction of the LGP, which is a one-dimensional distribution. So, the long strip micro-prism structure cannot modulate the light in the axial direction, resulting in large area identity in the width direction of the LGP, thereby the luminance uniformity of the BLM is affected. In this paper, a design idea of two-dimensional distribution of the micro-prism on the bottom surface of the PILGP, which improves the luminance uniformity of the BLM, is proposed to solve the problem that the luminance uniformity is affected by large area identity caused by one-dimensional distribution design of the micro-prism. The small length micro-prism structure is used to break the limit of the axial distribution of the long strip micro-prism structure, and it can modulate the light in the axial direction. The Lighttools software is used to optimize the two-dimensional distribution of the micro-prism on the bottom surface of a 5.0-inch PILGP. Comparing with the PILGP with one-dimensional distribution of the micro-prism on the bottom surface, the simulation results show that the utilization of light energy, illuminance uniformity and luminance uniformity in the BLM with optimized two-dimensional distribution of the micro-prism on the bottom surface of the PILGP respectively reach 92.03%, 87.07% and 91.94%, which meet industry standards. And the illuminance uniformity increases by 10%. Meanwhile, the luminance diagram shows that the overall luminance uniformity of the BLM is improved effectively. Moreover, the distribution principle of the micro-prism on the bottom surface of the PILGP is analyzed and the physical mechanism is reasonably explained . The simulation results above show that the design concept of the two-dimensional distribution of micro-prism is feasible. The study results have a certain referential value for the development of the BLM in light-weight and integration.