Parabolized stability equations (PSEs) were used to investigate the stability of boundary layer flows over a small hump. The applicability of PSEs to flows with a small separation bubble was examined by comparing the result with DNS data. It was found that PSEs can efficiently track the disturbance waves with an acceptable accuracy in spite of a small separation bubble. A typical evolution scenario of Tollmien-Schlichting (TS) wave is presented. The adverse pressure gradient and the flow separation due to the hump have a strong effect on the amplification of the disturbances. The effect of hump width and height is also examined. When the width of the hump is reduced, the amplification factor is increased. The height of the hump is found to obviously influence the stability only when it is greater than the critical layer thickness.