Focusing on the order allocation in vehicle logistics service supply chain, a bi-level programming model considering multiple modes of transportation was proposed. Firstly, considering that different transportation modes affect the transportation cost and the customer's on-time delivery requirement, a bi-level programming model aiming to punctual delivery and minimization of purchasing cost was established. Secondly, a Heuristic Algorithm (HA) was designed to determine the tasks of each transportation mode. Thirdly, Shuffled Frog Leaping Algorithm (SFLA) was used to solve task allocation of each transportation mode between functional logistics service providers. Finally, the solution of the proposed model was compared with those of Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO) through different scale examples. The results show that compared with the original purchasing cost 4.38 million yuan, the proposed model has a significantly optimized result 4.21 million yuan, which shows the order allocation scheme of the proposed model solves the order allocation problem of vehicle logistics more effectively. Experimantal results show that HA-SFLA can obtain the significantly optimized result quickly compared to GA, PSO and ACO, illustrating that HA-SFLA can solve the bi-level model considering transportation modes more efficiently. The bi-level order allocation model and algorithm considering transportation modes can reduce logistics costs while meet customer on-time requirements, making the logistics suppliers consider the transportation modes in order allocation phase to achieve more benefits.