To improve the accuracy of road safety evaluation, this article presents a method to calculate the average crash probability for highway sections based on fault tree and energy method. First, the average crash probability of sections was formulated based on fault tree theory, taking lateral instability, rollover, and rear-end crash into account. Second, an instability factor, which described the extent of steering instability and tire sideslip, was proposed based on energy method. Thereafter, the relationships between the instability factor and probability of lateral instability crash, the load transfer ratio and probability of rollover crash, the available sight distance and probability of rear-end crash were investigated. Then, the driver-vehicle-road multi-body dynamics model was developed based on the three-dimensional alignments of Ning-Luo Expressway using CarSim, the dynamics indexes such as lateral velocity, wheel vertical load were obtained, and the average crash probability of each section was calculated. Finally, the correlation between average crash probability and the average number of accidents was analyzed to validate the accuracy of the proposed method. Results reveal that the proposed method can improve the accuracy of evaluation results, compared with existing methods, thus providing theoretical basis for black spot identification of both design phase and in-service highways.