The atmospheric environment is an important factor affecting aircraft wake vortex decay and wake separation. In this paper, numerical calculations and strip modeling are combined to complete an analysis of wake encounter under three atmospheric stratifications expressed in Brunt–Väisälä (BV) frequencies. The SST k-ω turbulence model was chosen for the numerical simulation to complete the evolution of the wake vortex field of the A330 aircraft. The A320 and ERJ190 were selected as the aircraft for wake encounter analysis. The dimensionless roll moment coefficient (RMC) was selected as the indicator to construct a three-dimensional hazard zone for wake encounters and then calculate the wake separation. The results show that the higher BV frequencies correspond to faster wake vortex decay and hazard zone dissipation, and a slower decrease in the height of the hazard zone. The risk level of the ERJ190 is higher than that of the A320 with the same wake intensity, and the wake separation of the A320 following the A330 is 5516 m, which is 25.5% less than the ICAO RECAT separation standard, while the wake separation of the A330 following the ERJ190 is 5803 m, which is 37.6% less than the ICAO RECAT separation standard.