As China’s real estate market enters a period of in-depth adjustment, the stability of the real estate market and the transformation of urban development momentum have become important issues. Based on a nonlinear framework, this paper uses panel data of 286 Chinese cities from 2003 to 2016 and employs a threshold effect model to explore the impact of urban innovation on real estate market resilience (including investment resilience, sales resilience, and price resilience) and its mechanism of action. The results show that urban innovation has a significant positive impact on real estate market resilience, with a non-linear threshold characteristic: when the urban innovation index is below 0.043 9, the role of innovation in improving housing price resilience is limited; after exceeding this threshold, the promotion effect is significantly enhanced. Heterogeneity analysis finds that the positive effect of urban innovation on real estate market resilience has been more prominent since 2008, and in cities with a relatively high degree of real estate financialization, the supporting role of innovation in market stability is more crucial. In addition, the impact of economic factors such as labor scale and the proportion of the tertiary industry on real estate market resilience shows differentiated characteristics with the improvement of innovation level, while the greening rate of built-up areas always shows a positive impact. This paper can provide a theoretical basis and empirical support for the government to formulate policies of “innovation-driven real estate market resilience” and realize high-quality urban development.