Due to the increasing demand for passenger and freight transportation at the end of backbone lines, existing transportation modes cannot fully alleviate these transportation pressures. The low-speed maglev system can provide both passenger and freight services simultaneously. The system adopts unmanned driving and automatic loading and unloading technology, and can serve as an innovative, intelligent, and autonomous rail transit mode connected to the end of the backbone line. This article takes typical cities in China as an example to predict and analyze the demand for passenger and freight transportation at the end of their backbone lines. Next, define the concept of transportation organization mode for low-speed maglev system and divide it into four categories: single passenger transportation, single freight transportation, mixed passenger and freight line, and mixed passenger and freight formation. Finally, a comprehensive evaluation method for the transportation organization mode of low-speed maglev system based on FCE-AHP model was constructed. After calculation, the comprehensive scoring results of the transportation organization mode of LSM system were obtained as follows: mixed passenger and freight line, mixed passenger and freight formation, single passenger transportation, and single freight transportation. The research results of this article can provide reference for the future design, planning, and operation of low-speed maglev system.