The complex knowledge flow relationships in R&D projects introduce high levels of uncertainty, making reasonable buffer sizing crucial for absorbing project uncertainties and ensuring successful delivery. Based on this, this paper considers the knowledge flow relationships in R&D projects and proposes a method for determining the project buffer that incorporates the characteristics of knowledge networks. First, the impact of knowledge network structure on project buffer is analyzed from three dimensions: node position, inter-node relationships, and overall network structure. Next, the influence of knowledge network resilience on the buffer is assessed from the perspectives of structural resilience and functional resilience, followed by a comprehensive calculation of the project buffer size. Finally, Monte Carlo simulation is used for validation. The results show that, compared to classical project buffer determination methods, the proposed approach achieves dual optimization of both project duration and cost.