In the development of heterogeneous reservoirs, significant differences in reservoir permeability often lead to early water breakthroughs and ineffective water cycling during water injection, resulting in reduced recovery efficiency. Gel systems, as an effective profile control agent, can block high-permeability channels and improve oil displacement efficiency. However, current research on gel systems’ distribution and migration patterns in heterogeneous porous media mostly focuses on the macro scale, lacking in-depth exploration at the micro-scale. In this study, a microchip was designed to simulate the characteristics of heterogeneous porous media, and the micro-visualization experimental method was employed to directly observe the injection, migration, and distribution processes of the gel system. The influence of different injection rates on gel distribution is analyzed and clarified. The results show that the gel system primarily accumulates in high-permeability zones, followed by medium-permeability zones, with the least accumulation in low-permeability zones. Blocking high-permeability zones by the gel system alters the water flow direction in low-permeability zones, thereby improving the sweep efficiency of subsequent water flooding. As the injection rate increases, the distribution range of the gel in the microchip expands. This study clarifies the migration and distribution of gel systems in heterogeneous porous media at the pore scale, reveals the impact of injection rate on gel system distribution, and provides theoretical support and technical references for optimizing gel injection processes and enhancing the development efficiency of heterogeneous reservoirs.