Abstract: The boundary layer transition (BLT) of the HyTRV (Hypersonic Transition Research Vehicle) model exhibits complex three-dimensional characteristics. Experiments have been conducted in the Mach 6 low-noise wind tunnel named SKLA-TT1 to investigate BLT on the bottom surface of HyTRV model, specifically within the crossflow region and centerline region. Infrared thermography was used to obtain the transition front distribution at angles of attack of −2°, 0°, 2°, and 4°. High-frequency pressure sensors were employed to study the evolution of disturbance waves at 0° and 2° angles of attack. In addition, flow visualization and velocity field measurements were conducted using Rayleigh scattering and particle image velocimetry (PIV). It was found that a distinct ‘double-lobed’ transition front on the bottom surface was visualized by Infrared thermography. The transition region was divided into the crossflow region and the centerline region. At 0° case, high-frequency disturbances ranging from 200 to 500 kHz in the crossflow region were detected by high-frequency pressure sensors and visualized by Rayleigh scattering technique, which were determined to be the secondary instability modes of unsteady crossflow. No obvious dominant frequency was observed in the centerline region, whereas shear layers and vortex structures were obtained by PIV technique within the boundary layer. At 2° case, the amplitude of high-frequency secondary instability decreased with a frequency shifting towards lower bands compared to the 0° case, and the transition location in centerline region shifts upstream. Thus, it is found that BLT in the crossflow region is dominated by high-frequency secondary instability of unsteady crossflow. Increasing the angle of attack weakens the crossflow instability and makes the transition front move downstream. Conversely, transition along the centerline region is governed by streamwise vortex instability. Besides the transition onset moves upstream at higher angles of attack.