Introduction: Coronary microvascular dysfunction (CMVD), highly prevalent among patients with a mental disorder (anxiety or depression), is closely related to adverse cardiac events, including hospitalization, sudden cardiac death, and myocardial infarction. Shexiang Tongxin Dropping Pills (STDP), a traditional Chinese medicine, exerts endothelial protective function by anti-inflammation, anti-oxidative stress, and promoting blood circulation. STDP protects against CMVD in previous fundamental studies. The present trial is aiming at evaluating the effect of STDP on CMVD among depressed or anxious patients with non-obstructive coronary artery disease (NOCAD). Methods and analysis: Seventy-two depressed or anxious patients diagnosed with NOCAD combined with CMVD utilizing coronary artery angiography and stress cardiac magnetic resonance (CMR) will be recruited in the present study. These patients will be randomized into two groups, namely, Nicorandil group (Nicorandil combined with routine medicine), and STDP groups (STDP combined with routine medicine). The change of CMVD status by assessing absolute myocardial blood flow and myocardial reperfusion using stress CMR 3-month after discharge is defined as the primary endpoint. Major adverse cardiac events (MACEs), quality of life (QOL), and metal disorder improvement are defined as the secondary endpoints. Seattle angina questionnaire (SAQ) which is used to assess angina pectoris and QOL will be recorded at 1-, 3-, 6-, 9-, 12-month of follow-up. Seven-item Generalized Anxiety Disorder Scale (GAD-7) and 9-item depression module from the Patient Health Questionnaire (PHQ9) which utilized to evaluate anxiety and depression, respectively, will be recorded at 1-, 3-, 6-, 9-, 12-month of follow-up. This study will first evaluate the efficacy of STDP on CMVD among patients with a mental disorder and NOCAD, and discuss the potential mechanisms, providing therapeutic evidence for the STDP for these patients.