Against the backdrop of deepening global applications of artificial intelligence and a reshaping technological competition landscape, asset structure misalignment is distorting the allocation direction and intensity of corporate innovation inputs through multiple channels such as resource crowding-out and efficiency loss, becoming a structural bottleneck that constrains breakthroughs in key core technologies. Achieving innovation in critical core technologies cannot be realized without high-quality asset structure allocation. This study takes Chinese A-share listed companies from 2011 to 2023 as its sample and systematically investigates the impact mechanism of asset structure misalignment on firms’ innovation in key core technologies. The findings reveal that asset structure misalignment significantly suppresses innovation in key core technologies. Mediation analysis shows that this inhibitory effect operates primarily through three pathways: first, reducing R&D intensity; second, hindering human capital upgrading; and third, intensifying financing constraints. Heterogeneity analysis indicates that the negative effects of asset structure misalignment are more pronounced among large-scale enterprises, high-tech firms, companies with higher levels of AI application, growing-stage enterprises, and those located in regions with advanced financial technology development. Economic consequence analysis further demonstrates that asset structure misalignment reduces total factor productivity by weakening firms’ capacity for innovation in key core technologies. This research not only elucidates the formation logic and resource allocation distortion effects of asset structure misalignment at the theoretical level but also provides practical management insights and policy implications for enterprises striving to achieve breakthroughs in key technologies, offering significant real-world relevance for advancing China’s high-level self-reliance and strength in science and technology.