The atmospheric boundary layer is a crucial transitional region connecting the surface with the free atmosphere, playing a bridging role in land-sea-air interactions and the interactions between different atmospheric layers. This study utilizes rotary-wing UAVs, high-resolution lidar, and WRF simulation data to analyze the vertical distribution characteristics of temperature, humidity, wind speed, and wind direction boundary layer over the Mount Si’e region in 4–6 April 2024. The results indicate that the boundary layer temperature decreases with increasing altitude, reaching up to 18°C, while humidity decreases with height, dropping to as low as 35%. Daytime wind speeds range from 4 to 8 m/s, decreasing to 2 to 4 m/s at night. The boundary layer height can reach up to 900 m during the day and drops to 100–200 m at night, showing distinct diurnal variation characteristics. UAV observations are in good agreement with lidar and WRF simulation results, highlighting the application value of UAVs in high temporal and spatial resolution boundary layer studies. The study also reveals the significant impact of complex terrain on boundary layer characteristics, providing scientific insights into the dynamic and thermal processes of the boundary layer and offering reference value for improving regional weather forecasting and numerical simulations.