In recent years, green and low-carbon transformation has become a core imperative for promoting high-quality economic development, with improving carbon emission efficiency serving as a critical pathway. In this context, human capital—as a fundamental driver of development—should contribute significantly to enhancing carbon emission efficiency through the upgrading of its structural composition. However, while existing literature extensively investigates the relationship between aggregate human capital and carbon emissions, systematic research on how the upgrading of human capital structure affects carbon emission efficiency remains limited. In particular, there is a lack of in-depth analysis of the intrinsic transmission mechanisms and heterogeneous effects through which such structural changes influence carbon emission efficiency. This study measures the provincial-level upgrading of human capital structure using the vector angle method and evaluates carbon emission efficiency through the non-radial directional distance function (NDDF) model to examine the impact of human capital structure upgrading on carbon emission efficiency. Empirical results indicate that human capital structure upgrading significantly improves carbon emission efficiency across regions. Specifically, this effect operates primarily through channels such as fostering technological innovation and optimizing the energy consumption structure. Furthermore, regional technological capability, the degree of marketization, and the intensity of environmental regulation can amplify the positive impact of human capital structure upgrading on carbon emission efficiency. Compared to prior research, this paper offers three marginal contributions. First, it integrates human capital structure upgrading and carbon emission efficiency into a unified analytical framework, exploring pathways to improve carbon emission efficiency from the perspective of human capital structure advancement. Second, regarding mechanisms, it employs parallel multiple mediation analysis combined with the Bootstrap method to test whether human capital structure upgrading improves regional carbon emission efficiency through technological innovation and energy consumption structure optimization. This approach deepens the understanding of the intrinsic relationship between human capital structure upgrading and carbon emission efficiency. Third, given that the effect of human capital structure upgrading on carbon emission efficiency is moderated by marketization level, regional technology, and environmental regulation, this study further examines their roles in this relationship. These findings offer significant policy implications. This research partially unveils the intrinsic mechanisms through which human capital structure optimization drives carbon emission efficiency improvement. It provides a basis for policymakers to design targeted talent development and green transition synergy policies under the “Dual Carbon” goals framework. Additionally, it offers differentiated policy guidance for provinces at varying development stages to enhance the alignment between human capital and low-carbon technologies, thereby better leveraging human capital structure upgrading to serve regional green and low-carbon development.