Based on the panel data on 276 prefectural-level cities from 2011 to 2018, this paper uses longitudinal fixed effects models, panel threshold effects and instrumental variables to explore the relationship between digital economy development and human capital structure advancement. In addition, this paper examines how the development of the digital economy is related to human capital levels. The results show that digital economy development significantly boosts human capital structure advancement, as well as low-level and high-level human capital. However, the effect of digital economy development on midlevel human capital is not statistically significant. In terms of heterogeneity, we find that digital economy development significantly promotes human capital structure advancement in eastern and central-western regions of China, as well as in core and peripheral cities. Effects on the various levels of human capital show significant differences. Furthermore, digital economy development has a positive effect on human capital structure when industrial structure advancement is low. Past a certain threshold, however, the effect reverses. This paper suggests that each region should accelerate the development of digital infrastructure, rationally promote industrial structure advancement and boost the effectiveness of human resources to achieve high-quality economic development.