Objective: This study aimed to investigate the effect of early administration of heparin anticoagulation on blood flow and cardiac function in patients with acute ST segment elevation myocardial infarction (STEMI) treated with primary percutaneous coronary intervention (PPCI). Methods: A retrospective analysis was conducted on 730 patients with STEMI who underwent PPCI at the Department of Cardiology of the Chengdu Fifth People's Hospital of Chengdu from December 2017 to May 2023. According to the timing of heparin administration. The patients were divided into two groups based on the timing of heparin administration: the early group (3000 U unfractionated heparin administered immediately after the diagnosis of STEMI) and the delayed group (Intravenous injection of ordinary heparin 3000 U after successful interventional catheterization following the diagnosis of STEMI). The study compared general clinical data, myocardial injury markers (initial troponin, peak troponin, and tmax troponin), interventional related indicators (preprocedural thrombolysis in myocardial infarction (TIMI) flow grade, postprocedural TIMI flow grade, stent length, and thrombus aspiration), and postoperative indexes ST segment resolution (STR), left ventricular ejection fraction (LVEF), n-terminal pro-brain natriuretic peptide (NT-proBNP), major adverse cardiovascular events (MACE), and bleeding events. Results: The early group had a lower proportion of TIMI 0–1 grade and a higher proportion of TIMI 2–3 grade compared to the delayed group (p < 0.05). The early group showed better ST segment resolution (p < 0.05). There was no significant difference in LVEF and NT-proBNP classification between the two groups (p > 0.05). Subgroup analysis suggested an interaction between early heparin anticoagulation and left anterior descending infarct-related artery (IRA) on cardiac function. There was no significant difference in the incidence of MACE and bleeding events between the two groups (p > 0.05). Logistic regression analysis revealed that early heparin anticoagulation was a predictor of immediate TIMI grade 2–3 flow, and TIMI grade 2–3 flow was negatively correlated with early heparin anticoagulation. Conclusions: Early heparin anticoagulation can improve the patency of the IRA and myocardial perfusion in patients with STEMI. Additionally, it can reduce myocardial injury and improve cardiac function without increasing the risk of in-hospital bleeding.