Nutrigenomics is an emerging research field to investigate the interactions between food components and genes and elucidate their impacts on health and diseases. Exercise, another critical factor influencing human health, is intricately linked with nutrition and genetics, and is influenced by a combination of genetic background, lifestyle choice, and environmental factors. The high-throughput sequencing technologies and advanced bioinformatic tools have offered researchers to delve deeper into how individual genetic expression responses to exercise and how dietary interventions can enhance exercise performance and recovery through the gene expression changes and modifications. Among these mechanisms, gene expression emerges as the primary focus, highlighting its role in linking nutrients and exercise to metabolic pathways, muscle synthesis, and inflammation. While epigenetic modifications are briefly considered, the emphasis remains on how direct and indirect influences on gene expression drive physiological adaptations. Herein, the article reviews recent advancements in nutrigenomics within the context of exercise science, exploring gene-regulating mechanisms affected by specific nutrients and dietary patterns on exercise capacity, muscle synthesis, and damage repair. It also outlines the potential applications of personalized nutrition plans in athletic training and general fitness. In addition, this article addresses current challenges and potential issues in the practical implementation of nutrigenomics in exercise-induced health promotion. Future studies should emphasize interdisciplinary collaboration to unravel the intricate gene-nutrition-exercise interaction networks, thereby providing a solid theoretical foundation and technological support for the advancement of precision exercise nutrition.