The main paths of the knowledge diffusion network can reveal the important actors and diffusion process, which has an important significance in improving the efficiency of knowledge diffusion. Due to the independent path choice of project actors, knowledge diffusion networks show a dynamic characteristic in collaborative innovation projects. Taking into account this dynamic characteristic, dynamic main path analysis method for project context is proposed. The method, constructed by MATLAB simulation modeling, proposes calculation index and analysis strategies. Contrastive application of two main types of path analysis (the main path analysis method and dynamic main path analysis method) is carried out through a collaborative innovation project case, in order to verify the effectiveness and applicability of this method. The comparison results show that the main paths identified by the new method are more consistent with the actual main paths in knowledge diffusion practice, and the level of knowledge flow through main paths is higher. Therefore, our conclusion is that the dynamic main path analysis method proposed in this research has high applicability and accuracy for identifying the main paths in the collaborative innovation projects.