To address the difficulty in quantitatively evaluating the effectiveness of traffic organization schemes in highway reconstruction and expansion projects, this study proposes an evaluation system integrating traffic safety and operation efficiency. By combining VISSIM simulation with SSAM conflict analysis, this study verifies the effectiveness of the proposed evaluation method through a case study of the Guihua Interchange on the Chengnan Highway. For traffic safety evaluation, a safety risk assessment model is constructed, consisting of four first-level indicators (road, traffic, facilities, and management) and fifteen second-level indicators, along with a four-level risk classification standard. For operational efficiency evaluation, the Level of Service (LOS) and average delay are adopted for quantitative assessment. Simulation experiments are conducted on the three-stage traffic organization scheme for the Guihua Interchange in the Chengnan Highway reconstruction and expansion project. The results show that the comprehensive risk scores of the three-stage scheme are 12, 12, and 13, respectively, all classified as general risk. The peak-hour delay rates of the first and second stages are both lower than 6 s/(veh·km), verifying the feasibility of the temporary ramp and truck diversion strategy. The third-stage simulation indicates that the conflict rate of the east-south ramp reaches 0.58 conflicts/(veh·km) (93.5% of which are lane-changing conflicts). It is suggested to add graphical path indication traffic signs, paint no-lane-changing markings on the inner lanes, and guide ramp traffic flow in advance. The research demonstrates that the proposed evaluation system can effectively support the feasibility judgment, optimization path identification, and dynamic evaluation verification of traffic organization schemes, significantly improving the safety and approval efficiency of reconstruction and expansion projects.