Type 2 diabetes mellitus (T2DM) frequently coexists with obstructive coronary artery disease (OCAD), which are at increased risk for cardiovascular morbidity and mortality. This study aimed to investigate the impact of coronary obstruction on myocardial microcirculation function in T2DM patients, and explore independent predictors of reduced coronary microvascular perfusion. Cardiac magnetic resonance (CMR) scanning was performed on 297 T2DM patients {188 patients without OCAD T2DM(OCAD -) and 109 with T2DM(OCAD +)} and 89 control subjects. CMR-derived perfusion parameters, including upslope, max signal intensity (MaxSI), and time to maximum signal intensity (TTM) in global and segmental (basal, mid-ventricular, and apical slices) were measured and compared among observed groups. According to the median of Gensini score (64), T2DM(OCAD +) patients were subdivided into two groups. Univariable and multivariable linear regression analyses were performed to identify independent predictors of microcirculation dysfunction. T2DM(OCAD -) patients, when compared to control subjects, had reduced upslope and prolonged TTM in global and all of three slices (all P < 0.05). T2DM(OCAD +) patients showed a significantly more severe impairment of microvascular perfusion than T2DM(OCAD -) patients and control subjects with a more marked decline upslope and prolongation TTM in global and three slices (all P < 0.05). From control subjects, through T2DM(OCAD +) patients with Gensini score ≤ 64, to those patients with Gensini score > 64 group, the upslope declined and TTM prolonged progressively in global and mid-ventricular slice (all P < 0.05). The presence of OCAD was independently correlated with reduced global upslope (β =  - 0.104, P < 0.05) and global TTM (β = 0.105, P < 0.05) in patients with T2DM. Among T2DM(OCAD +) patients, Gensini score was associated with prolonged global TTM (r = 0.34, P < 0.001). Coronary artery obstruction in the context of T2DM exacerbated myocardial microcirculation damage. The presence of OCAD and Gensini score were independent predictors of decreased microvascular function. Retrospectively registered.