The three-dimension thermal distributions in double-cladding high-power Thulium-doped fiber amplifier(TDFA) with different inner-cladding shapes were achieved by solving the analytical thermal conductive equation with different inner-cladding boundary conditions. It indicates that the temperature difference induced by the overlap factor of double-cladding fibers(DCFs) with different inner-cladding shapes can be up to 107 K in the core. Moreover, the distance between the splice point and the position with maximum temperature relies on the ratio of the seed power to pump power and it can be 30 cm when pumped with 100 W and seeded with 10 mW. By analyzing the transverse and longitudinal thermal distribution, it is demonstrated that the offset DCF may be a better choice for TDFA due to its lower maximum temperature, high pump efficiency and Gaussian thermal distribution on the cross-section.