Currently, cross-border e-commerce logistics is lagging behind the development of infrastructure imperfections and other issues, so the realization of e-commerce logistics model innovation is a top priority. This paper firstly analyzes the innovation path of cross-border e-commerce logistics mode to shorten the logistics cost and improve the development efficiency of cross-border logistics chain by supply chain, logistics system, packaging, and localization. Secondly, it establishes a logistics operation demand forecasting model based on principal component analysis and radial basis function and introduces the composite system synergy model to measure the logistics matching ability and calculate the cross-border e-commerce logistics matching ability. Finally, quantitative analysis is carried out on three aspects of cross-border e-commerce logistics operations: demand, matching ability, and service effect. The results show that: the application of a cross-border e-commerce logistics model innovation path reduces the potential risk of cross-border express clearance, and the average timeliness of returned express shipment, goods arrival to delivery, product tariff tax rate across the border, and the complaint rate are reduced by 45, 0.5, 0.28, and 0.65 in 2019-2023. Meanwhile, the customer satisfaction is increased from 0.8416 to 0.9641. The cross-border e-commerce logistics model innovation path is proposed to meet the actual needs of social development.