The impact of rural-urban student mobility on the efficiency of resource allocation in China’s rural households is crucial for refining policies related to rural migrant settlement and the balanced allocation of urban and rural educational resources. Drawing on theoretical insights, this study employs a mixed methods approach—primarily qualitative, with quantitative support—to empirically test the impact of rural-urban student mobility on the resource allocation efficiency of rural households in China. Utilizing micro-survey data from China Family Panel Studies (CFPS), this study applies ordinary least squares (OLS) models, propensity score matching difference-in-differences (PSM-DID) models, and endogenous switching regression (ESR) models to ascertain the direction of this impact. Furthermore, this study incorporates in-depth interview data gathered from field research in D County to explore the dynamic mechanisms of resource allocation adjustments within these households. The results show that rural-urban student mobility significantly reduces the efficiency of labor resource allocation and agricultural production in China’s rural households. The impact is heterogeneous across different groups, most negatively affecting households with limited labor resources, lower educational levels, lower incomes, more productive fixed assets, and less self-owned land. Mobility leads to suboptimal occupational choices, resulting in decreased labor resource efficiency. Additionally, it distorts agricultural production by leading to labor loss, reduced investments in agricultural productivity, and misaligned land allocation decisions.