In this work, the cross-flow instability on the surface of a blunt elliptical cone with a long-short-axis ratio of 4∶1 is studied experimentally in the Mach 6 hypersonic quiet wind tunnel. Comprehensive use of temperature sensitive paint (TSP) technology, nano-tracer-based planar laser scattering (NPLS) technology and Kulite sensor pressure test to measure the temperature distribution in the cross-flow area on the surface of the model, boundary layer flow structure and model surface pressure are tested. The mechanism of boundary layer transition in the cross-flow control area on the surface of the elliptical cone is studied, and the influence law of incoming flow unit Reynolds number and angle of attack on boundary layer transition is obtained, and some conclusions are obtained below. In the wind tunnel noise mode, the transition of the boundary layer in the cross-flow area between the surface center line and the leading edge of the elliptical cone model with a length-to-short-axis ratio of 4∶1 is controlled by the traveling waves, and no footprint of the steady vortex is found. The characteristic frequency of the traveling wave is about 20 kHz. When the unit Reynolds number of the incoming flow increases, the transition position will be advanced, and the frequency and amplitude of the traveling wave will increase. Within a certain angle of attack, the transition position of the upwind boundary layer is delayed, and the characteristic frequency of the traveling wave does not change much but the energy is weakened. When the angle of attack continues to increase, the transition phenomenon disappears.