This paper studies the collaboration mechanism in the “main manufacturer-supplier” mode in the collaborative research and development(R&D) of complex products. According to the collaborative R&D attitude of the main manufacturer and the degree of the supplier's truncation to technology, we describe the perceived payment matrix of the main manufacturer and the supplier under different strategy selection conditions based on the prospect theory, and thus explore the behavior decision evolutionary process of both players. The results show that the main manufacturer and the supplier tend to underestimate the income and overestimate the financial risk of the complex products, due to the complexity and uncertainty of their cognitions of complex product R&D process. Thus, it is difficult for the supplier to achieve complete truncation to technology in the collaboration with the main manufacturer. Through the simulation analysis of evolutionary impact factors, we can see that the main manufacturer's collaboration attitude is affected by the perceived income, perceived financial risk, and income distribution coefficient of the final product, but less by the degree of technology truncation of the supplier. The degree of technology truncation of the supplier is affected by the risk distribution coefficient. These results provide a reasonable and valuable management implications for promoting the smooth progress of the “main manufacturer-supplier” collaboration mechanism.