The issue of boundary-layer transition with slight rarefaction for high-speed aircraft has recently received increased attention. In this paper, the stability and resonant interactions of boundary-layer waves for a Mach 5 flat plate under the slip effect are investigated using direct numerical simulation (DNS) and linear stability theory (LST). The slip effect is modelled by slip boundary conditions within the Navier-Stokes (NS) framework, and an LST method considering wall perturbations for both no-slip and slip flows is established. The present numerical results indicate that the slip effect has a consistent impact on the stability of fast and slow modes as obtained from DNS and current LST. In addition, the DNS results show that the slip effect delays the conversion of mode F1 to mode S led by their resonance, and enhances the resonant interactions between fast mode waves and fast acoustic waves.