This paper analyzes a problem processing mecha-nism in a new collaboration system between the main manufac-turer and the supplier in the “main manufacturer-supplier” mode, which has been widely applied in the collaborative development management of the complex product. This paper adopts the col-laboration theory, the evolutionary game theory and numerical simulation to analyze the decision-making mechanism where one upstream supplier and one downstream manufacturer must process an unpredicted problem without any advance contract in common. Results show that both players' decision-makings are in some correlation with the initial state, income impact coef-ficients, and dealing cost. It is worth noting that only the initial state influences the final decision, while income impact coeffi-cients and dealing cost just influence the decision process. This paper shows reasonable and practical suggestions for the manu-facturer and supplier in a new collaboration system for the first time and is dedicated to the managerial implications on redu-cing risks of processing problems.