In this paper, we study and analyze the characteristics of transportation vehicle scheduling problem in supply chain management with third party logistics enterprise. First, we subdivide all the transportation nodes into three distinct classifications. A novel partial collaborative transportation scheduling strategy is proposed based on two special kinds of transportation nodes which have integrated the self-support vehicle and 3PL vehicle resource. Then, depending on the transport mode of each kind of transportation nodes, a modified Ant Colony Optimization with negative selection operation (ACO-nso) with varying dimension matrix encoding and modified transition probability operation method has been presented. Finally, the simulative results demonstrate that the proposed approach is practical and efficient.