This study examines collaborative research and development (R&D) mechanisms within the context of import substitution supply chains. When faced with sudden disruptions in international supply chains, domestic manufacturers urgently need to find a domestic supplier to replace their overseas counterparts. However, domestic suppliers often lack the necessary capabilities to produce parts with equivalent technical specifications. To expedite import substitution, manufacturers must incentivize suppliers to increase R&D investment, posing a strategic decision problem in selecting the R&D mechanism. This study constructs a game-theoretic model to compare two collaborative R&D mechanisms—equity investment and cost-sharing—against a benchmark of no collaboration. Our analysis reveals that the cost-sharing mechanism amplifies R&D investment, while the equity investment mechanism may deter it. The optimal R&D mechanism depends on the difficulty of import substitution; the manufacturer favors the equity investment model for simpler scenarios, whereas cost-sharing is preferred for more arduous substitutions. In moderately complex situations, the manufacturer leans towards the cost-sharing mechanism. Notably, there are instances where the manufacturer prefers not to engage in collaborative R&D. Additionally, despite disparities in preferences between the manufacturer and supplier, win-win scenarios exist. These insights offer practical guidance for import substitution companies navigating collaborative R&D endeavors.