Background The national epidemiologic data in mainland China is still absent for moyamoya disease (MMD).Methods This study was a nationwide hospital-based observational retrospective study to estimate epidemiological characteristics of MMD. The data was based on the Hospital Quality Monitoring System (HQMS), a national database which covers all tertiary hospitals in mainland China. This system consistently collects medical records including demographic characteristics, diagnoses, procedures, and expenses etc. for all inpatients. MMD was identified by ICD-10 code (I67¢5) in HQMS.Findings A total of 47,443 new-onset patients with total 69,680 hospitalization records from 1312 hospitals during 2016 to 2018 were included. The annual incidence rate was 1¢14 per 100,000 inhabitants (95% CI, 1¢12−1¢16) and approximately a 2-fold increase from 2016 to 2018. The incidence in children (0¢18 per 100,000 inhabitants per year; 95% CI, 0¢17−0¢20) was significantly lower than that in adults (1¢40 per 100,000; 95% CI, 1¢38−1¢42) (P<0¢001) and the peak incidence was 45−54 years. The distribution model of incidence rate was presented as a clustered regional pattern (Moran's I = 0¢155, P = 0¢018, Z = 2¢375) by global spatial correlation analysis.Interpretation Our study reported the annual incidence of MMD was 1¢14 per 100,000 inhabitants in mainland China during 2016 to 2018, and it was increasing year by year. The geographical distribution of MMD incidence presented as a clustered regional pattern, which may provide new view for future study on the etiology for MMD.