This paper analyzed the effects of the problem size and the problem proposing mechanism on the decision-making processes, for the manufacturer and the supplier, regarding processing a problem in a new main manufacturer–supplier collaborative system using evolutionary game theory. Unpredicted problems may arise in the process of collaborative research and development (R&D) of complex products, like big passenger aircrafts, without any relative advanced contract, and either player will take risks to announce it. In addition to the factors of traditional cost and income, we take another two factors (i.e., the problem size and the problem proposing mechanism) into account in the examination of the problem processing mechanism. With evolutionary game theory applied, we can obtain the stable decision-making states of both players and how these two factors affect the problem processing mechanism. From the result, we find that the problem size has little effect on the two players’ decisions, while the problem processing mechanism has an impact when the experiences or the capacities of the manufacturer and the supplier are unbalanced. This paper contributes to manufacturer and supplier in a newly-established collaborative system to consider how to behave when unpredicted problems come.