Background: To investigate the effect and possible mechanism of obstructive sleep apnea hypopnea syndrome on coronary microcirculation in stable angina pectoris (SAP) patients with a single borderline lesion. Methods: We retrospectively analyzed 102 SAP patients with a single critical lesion [fractional flow reserve > 0.80] who were divided into an abnormal microcirculatory function group [index of microcirculatory resistance (IMR) ≥ 25, n = 52] and normal microcirculatory function (NMF) group (IMR < 25, n = 50). We compared indexes including biochemical indicators, coronary lesion characteristics, apnea hypopnea index (AHI), lowest oxygen saturation (LSaO2), night average heart rate, endothelin-1 (ET-1), nitric oxide (NO) and high-sensitivity C-reactive protein in serum between the two groups. Furthermore, risk factors affecting coronary microcirculation were analyzed. Results: There were no significant differences in biochemical indexes and coronary lesion characteristics between the two groups (p > 0.05). Compared to the NMF group, AHI (23.76 ± 8.41 times/h) and ET-1 (1.96 ± 0.43 ng/L) were obviously increased (p < 0.01), and LSaO2 (77.96 ± 7.26%) and NO (23.63 ± 7.09 mol/L) was significantly lower in the AMF group (p < 0.01). Moreover, AHI and ET-1 were positively associated with IMR (r1 = 0.887, 0.835, respectively). However, LSaO2 and NO had a negative correlation with IMR (r3 = 0.659, 0.691, respectively). Logistic regression analysis showed that AHI was an independent predictor of coronary microcirculatory dysfunction (odds ratio = 1.260, 95% confidence interval 1.083~1.467, p < 0.01). Receiver operating characteristic (ROC) curve analysis indicated an AHI cut-off value of 13.7 times/h to predict microcirculatory dysfunction (sensitivity 0.942, specificity 0.880). Conclusions: In SAP patients with a single critical lesion, AHI was associated with coronary microcirculatory dysfunction.