Instability evolution in a transitional hypersonic boundary layer and its effects on aerodynamic heating are investigated over a 260 mm long flared cone. 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 the parabolized stability equations (PSE) and direct numerical simulations (DNS). Four unit Reynolds numbers are studied, 5.4, 7.6, 9.7 and
. It is found that there exist two peaks of surface-temperature rise along the streamwise direction of the model. The first one (denoted as HS) is at the region where the second-mode instability reaches its maximum value. The second one (denoted as HT) is at the region where the transition is completed. Increasing the unit Reynolds number promotes the second-mode dissipation but increases the strength of local aerodynamic heating at HS. Furthermore, the heat generation rates induced by the dilatation and shear processes (respectively denoted as
) were investigated. The former item includes both the pressure work
and dilatational viscous dissipation
. The aerodynamic heating in HS mainly arose from the high-frequency compression and expansion of fluid accompanying the second mode. The dilatation heating, especially
, was more than five times its shear counterpart. In a limited region, the underestimated
was also larger than
. As the second-mode waves decay downstream, the low-frequency waves continue to grow, with the consequent shear-induced heating increasing. The latter brings about a second, weaker growth of surface-temperature HT. A theoretical analysis is provided to interpret the temperature distribution resulting from the aerodynamic heating.