The invention discloses an order transportation scheduling system and a scheduling method thereof, relates to the technical field of logistics order transportation scheduling, and aims to solve the problems that the efficiency is low and the working efficiency is influenced when transportation scheduling is carried out on existing warehouse logistics orders. The order transportation scheduling system comprises a control instruction terminal, an order inventory distribution module, an order transportation scheduling module, an order basic information module, an information processor, a material warehousing unit, a material ex-warehouse unit and an information input device, and the order inventory distribution module internally comprises order headers and order details. The order head-up comprises an ex-warehouse number, an order type, an order state, a delivery address, a delivery type self-pick-up, a delivery single person, an ex-warehouse date, a contact person, a contact way, a transportation requirement trunk line, a regular bus, co-allocation, a channel and express delivery.