The evolution of multi-mode instabilities in a hypersonic boundary layer and their effects on aerodynamic heating are investigated. Experiments are conducted in a Mach 6 wind tunnel using Rayleigh-scattering flow visualization, fast-response pressure sensors, fluorescent temperature-sensitive paint (TSP), and particle image velocimetry (PIV). Calculations are also performed based on both parabolized stability equations (PSE) and direct numerical simulations (DNS). It is found that second-mode dilatational waves, accompanied by high-frequency alternating fluid compression and expansion, produce intense aerodynamic heating in a small region that rapidly heats the fluid passing through it. As a result, the surface temperature rapidly increases and results in an overshoot over the nominal transitional value. When the dilatation waves decay downstream, the surface temperature decreases gradually until transition is completed. A theoretical analysis is provided to interpret the temperature distribution affected by the aerodynamic heating.