An effective method to control the non-linear shrinkage of micro-injection molded small-module plastic gears by combining multi-objective optimization with Moldflow simulation is proposed. The accuracy of the simulation model was verified in a micro-injection molding experiment using reference process parameters. The maximum shrinkage (Y1), volume shrinkage (Y2), addendum diameter shrinkage (Y3), and root circle diameter shrinkage (Y4) were utilized as optimization objectives to characterize the non-linear shrinkage of the studied gear. An analysis of the relationship between key process parameters and the optimization objectives was undertaken using a second-order response surface model (RSM-Quadratic). Finally, multi-objective optimization was carried out using the non-dominated sorting genetic algorithm-II (NSGA-II). The error rates for the key shrinkage dimensions were all below 2%. The simulation results showed that the gear shrinkage variables, Y1, Y2, Y3, and Y4, were reduced by 5.60%, 8.23%, 11.71%, and 11.39%, respectively. Moreover, the tooth profile inclination deviation (fHαT), the profile deviation (ffαT), and the total tooth profile deviation (FαT) were reduced by 47.57%, 23.43%, and 49.96%, respectively. Consequently, the proposed method has considerable potential for application in the high-precision and high-efficiency manufacture of small-module plastic gears.