Cardiovascular diseases (CVD) are major lethal diseases worldwide. Imbalance of gut microbiota (GM) homeostasis affects the development and progression of CVD. Exercise can remodel GM and improve GM disorders in CVD patients. By combing the research progress of GM-mediated exercise intervention for CVD, it was found that 1) Streptococcus, Lactococcus, Enterobacter, Klebsiella, and Turicibacter are pathogenic bacteria in CVD patients; 2) Response to exercise to modulate the microbiota of CVD includes increasing the abundance of beneficial bacteria such as Bifidobacteria, Lactobacillus, Bacteroides, Faecalobacteria, and Roseburia, decreasing the proportion of Streptococcus, Enterobacter, and other pathogenic bacteria, and regulating metabolite-producing bacteria such as Prevotella and Ruminococcus; 3) Exercise can improve the CVD process via GM, by remodeling physiological mechanisms such as vascular function, cardiac function, autonomic function and hemodynamics, and molecular mechanisms such as regulation of DNA methylation, histone modification, non-coding RNAs; 4) Most of the existing studies have focused on aerobic exercise. The specific mechanisms, individualized intervention programs and long-term effects of different types of exercise on GM in CVD patients need to be further explored.