It is difficult to determine the global optimal condition sequence and the location of the optimal condition conversion point of complex lines. In order to solve this problem, a multi-objective optimization method based on the improved sparrow search algorithm (ISSA) is proposed. The operation performance indexes and constraints of freight trains are analyzed, the optimization model with energy-saving punctuality is constructed, and the fitness function is designed based on linear weighted summation. According to the line speed limit and ramp conditions, a method for solving the working condition sequence of freight trains under complex lines is designed, and the position of the optimal working condition conversion point under the working condition sequence is obtained by the ISSA based on adaptive weight and Levy flight disturbance. The simulation results show that the target speed curve generated by the designed working condition sequence and the position of the conversion point can achieve energy-saving on the premise of meeting the on-time operation of freight trains.