Objective: This study aimed to explore the effect of pharmacist intervention on medication adherence, risk factor control, 6 months prognosis, and 2 years prognosis in patients with coronary artery disease (CAD) after the index percutaneous coronary intervention (PCI). Methods: From January 2015 to December 2015, 200 CAD patients were treated with PCI at our hospital. The control group was given routine treatment and nursing care. In addition to routine treatment and nursing care, the intervention group was given direct pharmacist intervention including medication program optimization, formulated pharmaceutical care, medication education, health education, and outpatient follow-up. The two groups were followed for two years. Readmission rate, incidence of major adverse cardiac events (MACE), readmission expense, awareness rate of secondary prevention drugs, medication adherence, and emotion management were compared between the two groups at 6 months and 2 years after the index procedure. Risk factors in the two groups at 2 years were compared. Results: At 2 years, the risk factors in the intervention group were significantly improved in comparison with the control group [smoking: 3.1% vs. 12.6%, P = 0.012; normal blood glucose rate: 79.6% vs. 62.1%, P = 0.007; normal blood pressure rate: 74.5% vs. 53.7%, P = 0.003; normal blood lipid rate: 84.7% vs. 57.9%, P < 0.001]. The readmission rate, MACE incidence, and readmission expense in the intervention group were significantly lower than the control group at 6 months and 2 years [47.7% vs. 72.6%, P = 0.001; 17.3% vs. 28.8%, P < 0.001; 7512.5 +/- 10269.6 RMB vs. 22172.6 +/- 24413.2 RMB, P= 0.025]. Conclusion: Pharmacist intervention can effectively improve medication adherence, reduce postoperative risk factors, MACE incidence, medical expenses in patients after the index PCI. These beneficial effects were increasingly more significant along with time.