Abstract: In order to achieve a completely coordinated cross-border logistics service supply chain, a two-level supply chain consisting of a cross-border logistics service provider and a logistics service integrator was constructed by applying Stackelberg game theory. Factor analysis is used to measure the level of customs clearance to analyze the impact of the level of customs clearance on the optimal decision and coordinated operation of the cross-border logistics service supply chain, and a contract mechanism designed for the perfect coordination of the cross-border logistics service supply chain. The research shows that considering the customs clearance level, the cross-border logistics service supply chain members and the overall profits of the supply chain can be improved. The overall profit of cross-border logistics service supply chain under centralized decision-making is always higher than that under decentralized decision-making. The revenue sharing contract can realize the Pareto optimization of cross-border logistics service providers and the overall decision-making of the supply chain, but it cannot achieve the complete coordination of the supply chain, while the two-part pricing contract model improved by Nash negotiation can achieve the complete coordination of the supply chain.