Intelligent connected vehicles (ICVs) are recognized as a new sustainable transportation mode, which could be promising for reducing crashes. However, the mixed traffic consisting of manually driven vehicles and ICVs may negatively affect road safety due to individual heterogeneity. This study investigated heterogeneity effects on freeway safety-based simulation experiments. Two types of vehicle dynamic models were employed to depict dynamic behaviors of manually driven vehicles and adaptive cruise control (ACC) vehicles (a simplified version of ICVs), respectively. Real vehicle trajectories were utilized to calibrate model parameters based on genetic algorithms. Surrogate safety measures were applied to establish the relationship between vehicle behaviors and longitudinal collision risks. Simulation results indicate that the heterogeneity has negative effects on longitudinal safety. With the higher degree of heterogeneity, longitudinal collision risks are increased. Compared to traffic flow consisting of human drivers only, mixed traffic flow may be more dangerous when the market penetration rate of ACC is low, since the ACC system can be recognized as a new source of individual heterogeneity. Findings of this study show that necessary countermeasures should be developed to improve safety for mixed traffic flow from the perspective of transportation safety planning in the near future.