Regional turbofan aircraft, which are used for medium-short distances, have a heightened risk of high-altitude Wake Vortices(VV) because of their tail-mounted engines and high horizontal tail configurations. For some regional medium-short-range turbofan aircraft, this threat is higher than that for conventionally designed aircraft. To analyze the flight safety of turbofan aircraft during cruise, this study developed a model to assess wake vortex encounters based on evolutionary high-altitude wake flow patterns. First, the high-altitude wake vortex aircraft dissipation patterns were analyzed by combining Quick Access Recorder (QAR) flight data with the wake vortex evolution model. Then, to consider the uniqueness of the medium-short-range turbofan aircraft, the severity of the wake vortex encounters was simulated using an induced roll moment coefficient. The proposed high-altitude wake vortex encounter model was able to identify and assess the high-altitude wake vortex changes, the bearing moments at different altitudes, and the atmospheric pressure conditions. Using the latest wake separation standards from the International Civil Aviation Organization(ICAO), acceptable safety wake intervals for follower aircraft in different scenarios were determined for the safety assessment. The results indicate that compared to mid and low altitudes, the high-altitude aircraft wake vortex dissipation rate is faster, the ultimate bearing moment is weaker, and the roll moment coefficient is higher, which confirm that there is elevated wake vortex encounter severity for regional turbofan aircraft. As safety is found to deteriorate when encountering wake vortices at altitudes higher than 8 km, new medium-short-range turbofan regional aircraft require higher safety margins than the latest wake separation standards.