The cross-flow perpendicular to the inviscid main flow in the boundary layer has potential instability, causing the transition from laminar flow to turbulent flow. In order to explore the mechanism of cross-flow in the blade boundary layer on transition, this paper studies the rectangular cascade of a certain compressor stator blade. Large eddy simulation calculations and flow display experiments for six attack angles with end wall cascades were carried out. It is found that the disturbance is dominated by the two-dimensional Kelvin–Helmholtz (K–H) instability. The transition begins at the position where the separation bubble begins to fall off into a two-dimensional K–H vortex and is completed where the K–H vortex breaks. The closer to the blade root, the later the transition occurs and the smaller the total pressure loss. The cross-flow velocity develops alternately between positive and negative, showing severe instability with more than 4 inflection points. The study on variable angles of attack shows that there is a superposition of two mechanisms, namely, separation bubble transition and cross-flow transition, at an angle of attack from −4° to 10°. In summary, although the separation bubble transition is dominated by K–H vortices, the occurrence of cross-flow instability is closely related to the transition position.