Under the background of accelerating the cultivation of new productivity, how to give full play to the role of the ballast stone of the patent system and effectively empower enterprises to make breakthroughs in key core technologies requires urgent attention. Based on the quasi-natural experiment of the patent fast pre-examination system, this paper examines the impact and mechanism of the patent examination system reform on enterprise key core technology breakthrough for the first time. The research shows that the patent examination system reform has effectively driven enterprise key core technology breakthrough, but has no significant impact on non-key core technology and strategic innovation. Reducing institutional transaction costs is an important way for the reform to play an incentive effect. The effect of reform is more obvious in enterprises with strong internal R&D foundation and regions with good external institutional environment. After the implementation of the reform, the breakthrough mode of the enterprise key core technology has the coexistence of independent R&D and cooperative R&D, but the latter is mainly based on the inter-enterprise cooperation mode, and the cross-border cooperation mode such as industry-university-research and government-enterprise is not yet mature. This study not only confirms the positive role of the patent fast pre-examination system in driving key core technological breakthrough, but also provides potential enlightenment for continuously deepening the reform and innovation of China’s patent system.