Changes in human body systems influence metabolism and may cause disease. The intestinal microbiota influence health and is itself influenced by factors including diet and drugs. Investigation of the relationship of the intestinal microbiota and chronic conditions like coronary heart disease (CHD) has been facilitated by advances in sequencing technology. Some studies have identified changes in the composition and the metabolism of intestinal microbiota in patients with CHD, including increases in phyla Bacteroidetes and Proteobacteria and decreases in phyla Firmicutes and Fusobacteria. The ratio of two metabolites of intestinal bacteria, trimethylamine and trimethylamine N-oxide, has been found to be related to CHD. This review summarizes recent research to provide ideas for further research on the relationships between intestinal microbiota and CHD and on the preventive measures for CHD.