Based on Grossman’s (1972) health model and Becker and Tomes’ (1979, 1986) cognitive ability family decision-making model, this study examines the impact and mechanisms of children’s left-behind status and parental return on the accumulation of children’s health and cognitive human capital. By extending these models, we derive that changes in left-behind status have both income and separation effects on children’s human capital accumulation. Using data from the China Family Panel Studies (CFPS), we employ a Propensity Score Matching with Difference-in-Differences (PSM-DID) model to investigate the impact of changes in left-behind status (either remaining left-behind or experiencing parental return) on children’s human capital accumulation. The research findings reveal the following: (1) Compared to non-left-behind children, left-behind status significantly decreases children’s health levels by 11.81%. In contrast, parental return significantly improves children’s health levels by 13.04% compared to children whose parents are away. All results are statistically significant. (2) The negative impact of left-behind status is more pronounced for primary school children, those residing in rural areas, and those with parents of lower educational levels, especially in western regions. In contrast, parental return has a more substantial positive impact on junior high school children, those living in rural areas, and those with parents of lower educational levels, particularly in western regions. (3) When analyzing the impact mechanisms, we find that although parental migration for work increases household income, leading to a positive income effect on children’s health, it does not fully offset the negative separation effect caused by parental absence. As a result, the overall effect remains negative. Based on these findings, for migrant worker parents, we propose tiered recommendations: ideally, parents should return home; alternatively, children should follow their parents. For the government, we suggest establishing comprehensive service centers for left-behind children based on actual needs. We recommend designing a holistic plan aimed at addressing the health issues of left-behind children through multi-level support measures.