Abstract: The change in angle of attack is one of the common variables under real flight conditions, and the resulting changes of the flow field cannot be ignored. To investigate the effect of angle of attack on three-dimensional boundary layer transition related to the instability of streamwise vortex, a typical elliptical cone model is selected in this paper to conduct wind tunnel experiments on the mechanism and its variation with angle of attack of boundary layer transition near the minor axis of the windward side. Based on TSP technology and NPLS technology, temperature rise curves along the streamwise direction and the fine structure images of the boundary layer both in the streamwise direction and transverse direction are obtained. The starting point of transition, the frequency of boundary layer disturbance waves, and streamwise vortex structure are analyzed with the changes of angle of attack. At the same time, based on pulsating pressure testing, the characteristic frequency and amplitude information of disturbance waves are obtained. The changes in disturbance wave characteristics with angle of attack explained the surface temperature rise and flow structure changes obtained from the flow display results. The main conclusions are as follows. Under the experimental inflow conditions, the boundary layer transition near the minor axis of the windward side of the elliptical cone is controlled by low-frequency instability. Within the range of angle of attack from 0°to 2°, the starting point of boundary layer transition and the characteristics of disturbance wave amplitude are insensitive to changes in angle of attack. When the angle of attack increases to 5°, the boundary layer can maintain stable growth of disturbance waves, and the transition is significantly delayed.