Aim To investigate and compare the immediate effect of intracoronary alprostadil and nitroglycerin injection in the treatment of coronary slow flow. Methods A total of 102 patients without obvious coronary angiography stenosis were selected, including 65 patients with coronary slow flow and 37 patients in the control group. Patients with slow flow were divided into nitroglycerin group (32 cases) and alprostadil group (33 cases) according to intracoronary drug injection. Baseline clinical data, coronary TIMI flow frames (TFC values), and TFC declines between the alprostadil group and nitroglycerin group were compared. Results There was no significant difference in baseline clinical data among the three groups except smoking (P＝0.02). Before injection, TFC values of the left anterior descending branch (LAD), circumflex branch (LCX) and right coronary artery (RCA) were significantly increased in alprostadil group and nitroglycerin group compared with control group (P＜0.05), but there was no significant difference in TFC values of the three coronary arteries between alprostadil group and nitroglycerin group (P＞0.05). After injection, the TFC values of LAD, LCX and RCA were significantly decreased in three coronary arteries in alprostadil group and nitroglycerin group compared with those before injection (P＜0.05). The decreased values of LAD, LCX and RCA in alprostadil group were 5.1,3.51 and 2.78 times of those in nitroglycerin group, respectively (P＜0.01). There was no significant difference in three coronary artery TFC values between the alprostadil group and the control group (P＞0.05). Conclusion Intracoronary injection of alprostadil or nitroglycerin can immediately improve coronary slow flow TFC value, and the effect of alprostadil is better than that of nitroglycerin.