Enzyme activity is crucial in biocatalysis, making methods to enhance enzyme performance a major focus of research. Computational design provides an efficient approach to boosting enzyme activity, thereby expanding its applications across various fields. This review highlights three main computational methods: molecular dynamics simulations, Rosetta, and machine learning, and explores recent advances in their use for rapidly enhancing enzyme activity in enzyme engineering. These techniques provide a novel perspective on enzyme activity optimization, significantly reducing the complexity of traditional screening processes. By integrating these advanced computational approaches, high-activity enzymes can be designed more rapidly, accelerating progress in protein engineering and synthetic biology.