Genetic variants in pre-microRNA (miRNA) genes or the 3'UTR of miRNA target genes could influence miRNA-mediated regulation of gene expression and thus contribute to the susceptibility and prognosis of human diseases. This study aimed to investigate the effect of 6 miRNA-related polymorphisms (miR-149 rs71428439, miR-146a rs2910164, miR-499 rs3746444, miR-423 rs6505162, miR-4513 rs2168518, and FABP2 rs11724758) on prognosis in 1004 patients with angiographic coronary artery disease (CAD). We found that miR-4513 rs2168518 was associated with blood pressure, triglycerides, total cholesterol, and fasting glucose levels, and risk of diabetes mellitus. miR-499 rs3746444 and miR-423 rs6505162 were associated with blood pressure and HDL levels, respectively. Both miR-4513 rs2168518 and miR-499 rs3746444 had significant impact on even-free survival. Furthermore, miR-4513 rs2168518 was associated with higher morality in CAD patients. In conclusion, miR-4513 rs2168518 and miR-499 rs3746444 might be potential biomarkers for the clinical prognosis of CAD.