The relationship between prothrombotic activity and coronary microvascular dysfunction (MVD) is limited. This study aimed to perform a comparative analysis of the relationship between prothrombotic activity and MVD in patients with myocardial infarction without obstructive coronary artery disease (MINOCA) and myocardial infarction with obstructive coronary artery disease (MI-CAD). Material and methods A total of 37 patients were enrolled in the study; the main group included 16 MINOCA patients, and 21 MI-CAD patients were included in the control group. Blood samples for protein C, antithrombin, WF, plasminogen, and homocysteine were performed on the 4th ± 1 day of admission. CZT-SPECT data were used to determine the standard indices of myocardial perfusion dis-orders (SSS, SRS, and SDS), as well as stress and rest myocardial blood flow (MBF), myocardial flow reserve (MFR), and difference flows (DF). MVD was defined as MFR (≤ 1.91 ml/min); coronary slow flow (CSF) was defined as corrected TIMI frame count (21 ± 3). Results We performed a step-by-step analysis of prothrombotic activity of the hemostasis system in binary logistic regression for MINOCA patients to identify factors associated with MVD (MFR ≤ 1.91 ml/min). A predictive model was developed to estimate the probability of reduced MFR. A low MFR is related to only plasminogen in MINOCA patients, whereas only wall motion score index (WMSI) in MI-CAD group was associated with a low MFR. Conclusion This small-scale study revealed the relationship between indicators of prothrombotic activity and MVD. The key factors that affect MVD in MINOCA patients was plasminogen, whereas, in patients with MI-CAD, WMSI was the key factor. Measurements of MVD may enhance the risk stratification and facilitate future targeting of adjunctive antithrombotic therapies in MINOCA and MI-CAD patients.