Background Since the 1990s, families from the ecologically hostile mountainous southern areas of Ningxia Province, China, have been migrating to the northern areas of the province. This study compared the prevalence of behavioral problems among migrant adolescents to those among host adolescents (adolescents from the northern areas) and adolescents in the region of origin (adolescents from the southern areas), to determine whether ecological migration is related to adolescent behavioral problems, and possible changes in such problems over time. Methods We used the Children and Adolescents Ecological Migration Survey on Mental Health, administered to 4805 students aged 12–16 years and their parents between 2012 and 2014 (W1), of whom 1753 students and their parents completed the follow-up between 2014 and 2017 (W2). Parents answered questions related to adolescent behavioral problems, main source of family income, parents’ desire to reverse migrate, improved standard of living, and parents’ educational attainment, while children completed the Eysenck Personality Questionnaire and a classroom environment questionnaire. Results The prevalence of behavioral problems among the migrant adolescents (28.04%) was significantly higher than among host adolescents (21.59%) or adolescents in the region of origin (24.37%; p < 0.001) at W1. After adjusting for gender and age, parents’ work outside the home was the main source of family income (OR = 1.42, 95% CI = 1.13–1.78), and adolescents’ learning burden (OR = 1.04, 95% CI = 1.01–1.06) in school negatively influenced behavioral problems. Strong student-teacher relationships (OR = 0.97,95% CI = 0.94–0.99) and parents who had no intention to move back to the original residence (OR = 0.70, 95% CI = 0.52–0.94) exerted a protective effect at W1; at W2, a protective effect was associated with improved living conditions (OR = 0.39–0.55, 95% CI = 0.25–0.84). The extent of behavioral problems among migrant adolescents significantly decreased after two years. Conclusion Ecological migration will increase children’s behavioral problems in the early stage, with various factors influencing the extent of these problems.

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