Background To evaluate the myocardial microcirculation perfusion of patients with acute ST-segment elevation myocardial infarction (STEMI) with a different index of microcirculatory resistance (IMR) after percutaneous coronary intervention (PCI) by myocardial contrast echocardiography (MCE) and analyse the value of MCE in predicting myocardial perfusion after PCI. Methods Fifty-six patients with acute STEMI who underwent an emergency PCI were selected from October 2018 to October 2019 in our hospital. According to the IMR values measured during PCI treatment, the patients were divided into three groups. Traditional ultrasound and MCE were performed one week after PCI. The left ventricular ejection fraction (LVEF), ventricular wall motion score index (WMSI), A value, β value and A × β value (which refers to the patient’s myocardial blood flow) were measured. The receiver operating characteristic curve was drawn to evaluate the effectiveness of the MCE parameters in the diagnosis of myocardial microcirculation perfusion disorders. Results The results showed that there was no significant difference in the LVEF among the groups. The WMSI in Group 3 was statistically different from that in Groups 1 and 2 (P < 0.05), but there was no statistically significant difference in the WMSI between Groups 1 and 2. Among the three groups, the A value, β value and A × β value were significantly different (P < 0.05). According to Spearman’s correlation analysis, the MCE quantitative parameters (i.e. the A value, β value and A × β value) were negatively correlated with the IMR value (r = −0.523, −0.471, −0.577, P < 0.01). Conclusions The A value, β value and A × β value were negatively correlated with the IMR value. Furthermore, MCE could be used to observe the myocardial perfusion in patients with acute STEMI after PCI and may be one of the indicators used to accurately evaluate myocardial microcirculation.