Inter-cell manufacturing could quickly respond to market changes and save investments on equipment. The number of vehicles in an inter-cell manufacturing system is one of important factors affecting results of inter-cell scheduling and related costs. Previous literatures on inter-cell scheduling with limited transportation capacities assumed that numbers of vehicles in a manufacturing system are fixed and simply set as numbers of manufacturing cells. However, numbers of vehicles generally are determined by decision makers and might be different in different manufacturing systems. Reducing the number of vehicles could save investments and latter operation costs. To help decision makers make decisions on the number of vehicles, it is needed to explore relationships among the number of vehicles, makespan, and total costs. An inter-cell scheduling model is proposed for an inter-cell manufacturing system with flexible routes and limited transportation capacities to optimize the number of vehicles, makespan and total costs. A Shuffled Frog Leaping Algorithm (SFLA) is designed to solve the proposed model. A four-segment coding method is proposed to encode operation sequence of parts, manufacturing cells, and machines for processing operations, and vehicle allocation. A case is used to analyze relationships among the number of vehicles, makespan, and total costs. Conclusions are yielded, which would help decision makers to make decisions on the number of vehicles.