Amidst complex and severe internal and external shocks, China and the US have both recognized the importance of enhancing the resilience of basic research innovation. This paper defines the concept of resilience in basic research innovation and measures it for China and the US using the core variable method, based on Web of Science publication data from 2002 to 2022. It further explores the characteristics, regional differences, and dynamic evolution of this resilience using the Dagum Gini coefficient and kernel density analysis. Key findings include: the US experiencing a downward trend in resilience, while China's resilience remains relatively stable and stronger overall; the US showing a more balanced regional distribution of resilience under financial and pandemic shocks, whereas China exhibits greater regional disparities; the US witnessing declines in both resistance and recovery capabilities over time, while China sees an increase in resistance but a decrease in recovery capabilities, with a significant positive correlation between resistance and recovery in China, unlike in the US. Additionally, the US has a more balanced distribution of published papers across major regions, while China shows a polarized trend. The resilience performance of major regions in both countries varies under different shocks. The Dagum Gini coefficient indicates that the overall gap in resilience between China and the US is widening, driven by domestic differences during the resistance period and by inter−country differences during the recovery period. Kernel density estimates reveal that the US has declining resilience with increasing inter−state differences, polarization during the resistance period, and convergence towards lower levels during the recovery period. In contrast, China has higher resilience with decreasing inter−provincial differences and a reduced proportion of low−level regions.