Innovation is an eternal theme of human development, and green innovation efficiency serves as the basis for achieving innovation-driven development in a country or region, as well as an important aspect of ecological civilization construction. In this context, based on the panel data of 30 Chinese provinces during 2003–2020, this study explores the effect of housing price bubbles on green innovation efficiency by using a global SBM-DEA model with unexpected outputs and a two-way fixed effects model. The results show that housing price bubbles considerably reduced green innovation efficiency, which is also verified by a series of robustness and endogeneity tests. Heterogeneity tests show that housing price bubbles in eastern and high human capital regions have a significantly higher inhibitory effect on green innovation efficiency than that in the central and western regions and low human capital regions. The mechanism test shows that housing price bubbles have reduced green innovation efficiency by intensifying the mismatch of labor and capital between regions. Moreover, high housing prices will further deepen the negative impact of housing price bubbles on green innovation efficiency, while expanding economic openness will help alleviate the negative impact. Therefore, to effectively enhance regional green innovation efficiency, we put forward a series of policy measures in terms of strengthening the adjustment of housing policies, optimizing the resource allocation structure, and implementing differentiated environmental control tools.