Plastic injection molding is one of the most popular manufacturing processes for mass production, and optimizing the mold cooling system is critical for reducing the cycle time and improving the final part quality. Conventional cooling simulation uses the boundary element method to perform the cycle-averaged analysis, which is a simplification due to computational resources limitation. This paper develops a three-dimensional transient cooling simulation method based on the finite element method, which can simulate the complex mold system accurately and efficiently. It is shown that this method finishes the transient cooling analysis in 478 seconds on the real-world injection molding mold with more than 6.9 million tetrahedral elements. Its accuracy is compared against the experimental results with the maximum temperature error less than 4%, and the average temperature error less than 1%.