In order to examine the potential correlation between heat and helium isotope signatures in a non-volcanic region, we estimated the local heat flux using Peclet number analysis of the thermal profiles from of deep, vertical boreholes in the Kii Peninsula, Southwest Japan. There is a distinct correlation between the common logarithms of the 3He/4He ratios and heat flux. Hot springs with 3He/4He ratios higher than the expected value of 3.4 RA, which is attributed to mantle helium trapped in igneous intrusions of Middle Miocene age, have heat flux values higher than 90 mW/m2. Upward flow of deep fluids predominates over the groundwater recharge of the local hydrology there. These results support the hypothesis that the hot springs with significantly higher 3He/4He ratios in the Kii Peninsula originate due to the effective transfer of mantle helium through the crust, dominantly by advection associated with ascending high temperature, deep fluids along mantle-derived volatiles.