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Abstract Background Ecological migrants has a special background compared with other types of migrant. However, the mental health status of ecological migrants who were expected to benefit from a massive "ecological migration project" initiated by the Chinese government is unknown. This study aims to explore the influence of environmental change on individuals' mental health and to improve current understanding of the mechanisms that mental disorders occurred. Methods The data were extracted from a cross-sectional study. Anxiety disorders, mood disorders and substance use disorders were assessed using the Chinese version WHO-CIDI. The prevalence of mental disorders was stratified by migration status into ecological migrant, local resident and original resident groups. Unconditional logistic regression models were used to calculate the risk of prevalence among these three groups. Results After controlling for gender, ethnicity, age, marriage, and education, the migrants had lower risk of mental disorders than original residents [OR = 0.70 (95 % CI: 0.57–0.86)], p < 0.001), but had a higher risk of mental disorders than local residents [OR = 1.29 (95 % CI: 1.06–1.55)], p = 0.007). Conclusion The ecological migration project may be beneficial to people's mental health by improving their living environment and social economy.