Under the background of open innovation, with the shortage of resources and the increasing requirements for technical complexity, collaborative innovation has become an important means for enterprises to improve their core capabilities. This paper takes high-tech enterprises for example, explores the factors affecting the core competence of high-tech enterprises under the collaborative innovation mechanism by studying structure model and combining it with knowledge management theory, and draws the following conclusions:(1) Collaborative innovation mechanism and enterprise's strength are essential; (2) The relationship between the "six major players" under the collaborative innovation mechanism affects the core competence by changing the efficiency of collaborative innovation and the strength of the enterprise; (3) Knowledge absorption, knowledge integration and knowledge utilization have an impact on core competencies; (4) Political, economic, social and market factors have different degrees of impact on core competencies. Those conclusions provide theoretical basis and recommendations to improve the core competence of enterprises, which are indeed challenging from the perspective of collaborative innovation.