Abstract Background Despite the plausible physiological connection between the index of microvascular resistance (IMR) and fractional flow reserve (FFR), a comprehensive understanding of their correlation is lacking. Purpose This study aims to elucidate the association between IMR and FFR in patients presenting with angina and non-obstructive coronary artery disease, employing various IMR threshold values. Methods Consecutively enrolled patients with angina and non-obstructive coronary artery disease underwent a thorough functional assessment encompassing both epicardial (Pd/Pa, FFR) and microvascular (coronary flow reserve, CFR; IMR) domains by the thermodilution technique. The hyperemic response to adenosine (Δ) was quantified as the disparity between Pd/Pa and FFR. Correlations between FFR and IMR, as well as between Δ and IMR, were examined globally and categorized based on the presence of coronary microvascular dysfunction (CMD, CFR<2). Subsequently, patients were stratified into three groups based on IMR values: Group 1 (IMR<25), Group 2 (25≤IMR<40), and Group 3 (IMR ≥ 40). Further analyses of adenosine hyperemic response, IMR, and FFR correlations were conducted within each group. Results A total of 116 patients and lesions were evaluated, with 71 in Group 1, 32 in Group 2, and 13 in Group 3. Globally, FFR showed no correlation with IMR (r = 0.025, p = 0.788), regardless of CMD presence (CMD, r = 0.210, p = 0.325; no CMD r = -0.051, p = 0.631). Same results were observed for the relationship of hyperemic response to adenosine and IMR (r = -0.0398, p = 0.673). However, upon stratification by IMR values, only patients in Group 3 exhibited a positive correlation between FFR and IMR (r = 0.580, p = 0.037), with a notable reduction in the hyperemic response to adenosine as IMR values increased (r = -0.5485, p = 0.052). After adjusting for potential confounding factors, a significant increase of 0.01 in FFR values was observed for every 10-unit rise in IMR (p = 0.045) in this Group. Conclusions FFR appears to be particularly influenced by elevated IMR values (≥40). Prudent interpretation of FFR values in such instances is imperative, especially in cases of functionally borderline epicardial stenosis.