In recent years, uncertain events such as financial crisis, trade frictions, and an outbreak of COVID-19 have occurred frequently, which have made economic development face severe tests, so the issue of regional economic resilience has attracted much attention. As the link between industrial structure and economic growth, innovation capacity has an essential impact on economic resilience. Based on measuring the economic resilience of 31 provinces (municipalities and autonomous regions) in China from 2008 to 2019, this study uses the Entropy-Tobit model to analyze the specific role of innovation capacity impact on economic resilience. The findings confirm that the overall level of China’s economic resilience has increased annually, with significant regional differences: the Eastern is higher than the Western, and the high-value regions have been shifting from north to south. Innovation capacity is positively correlated with economic resilience, and the magnitude of its effect is influenced by industrial structure with a regional, which means that regions with a higher degree of industrial specialization have a relatively weaker ability of innovation capacity to enhance economic resilience. Thus, to strengthen the ability of Chinese regions to cope with risks, regions need to focus on fostering innovation capabilities, optimizing industrial structures, and building supporting economic systems.