(1) To estimate the pooled prevalence of psychological symptoms in Chinese migrant workers (CMWs), as measured using the Symptom Checklist-90-R (SCL-90-R) in observational studies conducted in China, and (2) to explore the potential variables associated with the SCL-90-R Global Severity Index (GSI), the overall mental health indicator of CMWs. We performed a comprehensive literature search of the major English and Chinese databases (to June 2012). Cross-sectional surveys and case-control studies of CMWs (and controls where appropriate) that reported at least one subscale score of the SCL-90-R were included. Multilevel meta-analysis was used to pool the symptom scores of cross-sectional surveys and mean differences of symptom scores ("Cohen's d" values) between CMWs and controls of case-control studies. Multilevel meta-analysis with ecological- or study-level covariates was used to explore the associations between variables and SCL-90-R GSI score. The search yielded 48 cross-sectional surveys (comprising 42,813 CMWs) and seven surveys that included control samples. The pooled psychological symptom scores (95% confidence interval) of CMWs were statistically higher than those of norms from Chinese general population on all scales of SCL-90-R, except for obsessive-compulsive subscale in study quality subgroup analysis. CMWs also scored statistically higher than those of urban counterpart controls on all scales of SCL-90-R. Multilevel regression meta-analysis model revealed that four covariates that accounted for 33.9% of SCL-90-R GSI heterogeneity across all surveys, including: "mean age of study sample," "geographic area," "per capita GDP," and "statutory minimum monthly wage" of study site in implementation year. CMWs have more severe psychological symptoms than the general population, and thus, appear to experience higher level of psychological distress. Macro-economic factors may have impact on the overall mental health of CMWs, but the factors that contribute to mental health and mental distress among CMWs remain to be explored and understood.