Taking the expressway network for hazardous materials (HAZMAT) transportation as the research object, the starting point of controlling the total risk was introduced. By drawing on the principle of sub-optimal tolling, the tolls on road sections were taken as decision variables, a bi-level programming model with variational inequality was established for the optimization research of HAZMAT transportation management. A particle swarm optimization algorithm nested with a diagonalization algorithm was designed to solve the proposed model, and a case was used to verify the calculation. The corresponding numerical results and parameter sensitivity analysis show that the proposed bi-level programming model and corresponding algorithm for tolling of expressway transportation networks for HAZMAT are effective and feasible, which can provide a reasonable decision-making reference for the government’s HAZMAT transportation management department.