Background: Prevalence estimates of major depressive disorder (MDD) among adults in China have varied widely between studies. In this systematic review and meta-analysis, the overall prevalence of MDD in the Chinese population was estimated from published epidemiological studies and potential moderators that account for variability in estimates were assessed. Methods: A systematic literature search was conducted in PubMed, EMBASE, Web of Science, PsycINFO, China National Knowledge Internet (CNKI), and WanFang databases to identify relevant studies. Data analyses were conducted using the Comprehensive Meta-Analysis Version 2.0. Results: Forty studies comprising 1,024,087 subjects were included. The pooled point, 12-month, and lifetime prevalence rates of MDD in China were 1.1% (95% CI: 0.9–1.4%), 1.6% (95% CI: 1.0–2.5%), and 1.8% (95% CI: 1.5–2.2%), respectively. Subgroup and meta-regression analyses revealed gender, marital status, survey year, being published in English language, use of the Diagnostic and Statistical Manual of Mental Disorders (DSM) diagnostic systems and age as significant moderators of MDD prevalence. Conclusion: The overall prevalence of MDD in the Chinese population appears to be lower than that of most countries, but the rates have been increasing over time and are elevated in particular demographic subgroups. Due to the negative consequences of MDD, effective preventive measures, early identification, and timely treatments are still important and should be offered to those in need.