This study assessed the early social-emotional development of left-behind children (LBC) in rural China and determined the mediating factors linking parental migration to LBC's developmental outcome. We used cross-sectional data of 845 LBC under 3 years old from five counties in rural China in 2018. Social-emotional problems were assessed by the ages and stages questionnaires: social-emotional. Family structure, function, and child nurturing care practices were measured to explore their roles in potential pathways of parental migration affecting early social-emotional development. 36.4% of LBC were identified with social-emotional problems; the rate was higher among LBC with migrant parents than those with migrant fathers (39.9% vs. 30.5%, adjusted OR: 1.40 [95% CI 1.01, 1.93]). Results of structural equation modeling reveal that caregivers' low education and depressive symptoms, poor migrant-caregiver communication, family poverty, and no assistant caregiving weakened home parenting environment, and then contributed to LBC's social-emotional problems. LBC in early childhood may be at a high risk of social-emotional problems, which are primarily caused by the transition of family structure and function and consequently weakened home environment.