Abstract: The fundamental secondary instability mode can be observed in the earlier stage of hypersonic boundary layer transition in recent direct numerical simulations and quiet wind tunnel experiments, which suggest the existence of streamwise streaks. This study investigated the generation mechanism of these streaky structures and their inviscid instability. In order to simplify the problem, the hypersonic boundary layer over a flat plate was focused on, and the instability was analyzed using both the linear stability theory (LST) and the secondary instability analysis (SIA). The results suggest that the dominant secondary instability mode can be affected by the amplitude of the two-dimensional primary mode (the second mode). When its amplitude is large, the fundamental mode is the dominant one, and mainly consists of streamwise streaky structures, or streamwise vortices. Inviscid bi-global analysis was used to investigate the instability of the streaks, and multiple inviscid modes were identified. The modes with lower frequencies can be seen as the extension of the first mode, and those with higher frequencies correspond to the second mode induced by the compressibility. This work makes a contribution on understanding the mechanism of hypersonic boundary layer breakdown.