Heat flux measurement in a hypersonic wind tunnel is one of indispensable requirements for designing the next generation re-entry vehicle. Heat flux is usually calculated from a temporal change in temperature on the model surface. Temperature-Sensitive Paint (TSP) is a global temperature measurement technique based on photochemical reaction. This technique was applied to a hypersonic shock tunnel test, but there existed uncertainties caused by TSP layer thickness. In this study, the relationship between TSP layer thickness and measurement accuracy in heat flux was investigated by experiment. The models were tested at Mach 10 in the JAXA 0.44-m Hypersonic Shock Tunnel and heat flux caused by aerodynamic heating on the model surface was measured. A comparison between TSP data and conventional thermocouple data showed that the measurement error changed with the layer thickness in nonlinear fashion. To demonstrate the capability of TSP with the optimized thickness, tests using a 3-dimensional wing-body model have been conducted and the complicated heat flux pattern caused by shock-wave/shock-wave interaction has been observed.