To improve the safety and efficiency of freeway under the management of partition speed limit and reduce drivers’ burden caused by improper speed limit and frequent speed changes, this research optimized and coordinated freeway speed limit sections under the management of partition speed limit. First, the optimal coordination model for freeway speed limit was constructed in three cases on the basis of the principle of minimum loss time. Second, the minimum length of the speed limit section and the number of speed limit sections used in the process of the coordinated optimization were determined based on the theoretical calculation of drivers’ cognitive distance, psychological stability distance, speed limit sign front distance, and a questionnaire survey. Then the risk function and income function were used to characterize the traffic safety and efficiency of freeway and construct the corresponding evaluation model. Finally, the effectiveness of the proposed method was tested by simulating the original setting of the speed limit section and the traffic condition of a project freeway. Results show that after the optimization the comprehensive safety index decreased by 45.51% and the comprehensive efficiency index increased by 26.78%, which means the state of safety and efficiency has come closer to the ideal point (a, b). This feasible and effective method can improve traffic safety and efficiency level, and provides a theoretical basis for the safety and efficiency management of speed limit sections.