The establishment of an evaluation model for bus operation efficiency is crucial in determining the bus routes along the rail transit line that require optimization, laying the theoretical foundation for the integration of the two networks. Firstly, a qualitative and quantitative method was used to select bus routes that have a high correlation with the rail transit system and are of research significance. Secondly, an evaluation system was constructed based on the rationality of the bus network itself and the synergy between the two networks. Finally, the Pareto optimal cross-efficiency model was employed to determine the operation efficiency of the bus routes along the rail transit line. Taking the example of Line 1 in Nanchang, 25 bus routes along the line were identified and empirically analyzed. The results indicated that the Pareto optimal cross-efficiency model's score was more readily accepted by all Decision-Making Units (DMUs). The data analysis revealed that the bus network in Nanchang exhibited good self-rationality. However, in terms of synergy between the two networks, there is room for improvement by optimizing route directions and adjusting route duplication coefficients to enhance their collaborative nature. Finally, this paper is based on the Pareto cross-efficiency mean values of both factors, the 25 bus routes were categorized into four cases, providing practical and valuable insights for the managers and decision-makers of the public transportation system.