Pallet pooling has been widely recognized as an important part of the green supply chain. The development of pallet pooling is an essential component for the transformation and upgrade of the logistics industry in China. Pallet pooling can, however, lead to a conflict over potential benefits among the players. One of the main problems of pallet pooling in China is the reasonable benefit allocation mechanism has not been formed. The pallet pooling system (PPS) with participation of the third-party platform (PPSWPTPP) is one of the pilot modes of pallet pooling in China. Based on evolutionary game theory and a penalty mechanism for breach of contract, this paper constructs a tripartite evolutionary game model of the PPSWPTPP. Eight propositions are set in two basic scenarios regarding whether pallet pooling is adapted to the logistics market to study the stability and dynamic evolution process of the players in the PPSWPTPP. Theoretical and numerical simulation results indicate that these will affect the smooth development of the PPS. The suitable setting of penalties and bonuses, the precise estimation of the pooling benefits, the intention intensity of the players to the pallet pooling, and whether to adapt to the logistics market demand are explored.