This paper mainly studies the joint decision of transportation mode and path in the multi-mode transportation network to provide the optimal plan for freights. This paper constructs a multi-mode transportation network system by setting virtual connections between networks with different transportation modes. The Dijkstra and multi-objective optimization algorithms are used to select the path in the network. After determining the optimal path, the paths’ time, cost, and risk functions are established. The multi-objective function is converted into a single objective function by setting constraint conditions through the analytic hierarchy process. Then, the function is optimized by using the gradient descent method. Finally, the transportation plan for the case of chemical freights is formulated by using the above algorithms. The results show that the proposed algorithm can successfully find the solution for the joint decision of transportation mode and path in the complex network. After a quantitative analysis of the planned effect, the optimization actions of changing the initial transportation time and adjusting the upper limit of resources are proposed. The study findings provide a theoretical basis for improving the efficiency of the comprehensive transportation network.