This paper was aimed at finding out the solution to the problem of insufficient dimensional accuracy caused by non-linear shrinkage deformation during injection molding of small module plastic gears. A practical numerical approach was proposed to characterize the non-linear shrinkage and optimize the dimensional deviation of the small module plastic gears. Specifically, Moldflow analysis was applied to visually simulate the shrinkage process of small module plastic gears during injection molding. A 3D shrinkage gear model was obtained and exported to compare with the designed gear model. After analyzing the non-linear shrinkage characteristics, the dimensional deviation of the addendum circle diameter and root circle diameter was investigated by orthogonal experiments. In the end, a high-speed cooling concept for the mold plate and the gear cavity was proposed to optimize the dimensional deviation. It was confirmed that the cooling rate is the most influential factor on the non-linear shrinkage of the injection-molded small module plastic gears. The dimensional deviation of the addendum circle diameter and the root circle diameter can be reduced by 22.79% and 22.99% with the proposed high-speed cooling concept, respectively.