Parts with microstructure arrays have been widely used in biotechnologies and optical technologies, and their performances are affected by replication uniformity. The uniformity of the microstructure is still a challenge in micro-injection molded parts and is greatly affected by the cavity thickness and process parameters. In this study, the replication uniformity of microstructures is experimentally investigated. The relationship between the replication uniformity and cavity thickness was explored through single-factor experiments. Additionally, the impacts of the process parameters on the replication uniformity were also studied through uniform design experiments. A regression equation was established to describe the quantitative relationship between the important parameters and replication uniformity. The results showed that the replication uniformity of microstructures increases by 39.82% between the cavity with the thickness of 0.5 mm and a cavity of 0.7 mm. In addition, holding time is the most significant factor influencing the replication uniformity, followed by mold temperature, melt temperature, and injection speed. It is concluded that the thickness of cavity and the process parameters have significant influence on the replication uniformity. The experimental results provide important data on how to improve the replication uniformity of parts with microstructure arrays.