The distribution of substrate temperature plays a decisive role on the uniformity of polycrystalline diamond films on cemented carbide tools with a long flute, prepared by a hot filament chemical vapor deposition (HFCVD). In this work, the heat dissipation mode at the bottom of tools is a focal point, and the finite volume method (FVM) is conducted to simulate and predict the temperature field of tools, with the various materials of the holder placed under the tools. The simulation results show that the thermal conductivity of the holder affects the temperature difference of the individual tools greatly, but only affects the temperature of different tools at the same XY plane slightly. Moreover, the ceramic holder can reduce the difference in temperature of an individual tool by 54%, compared to a copper one. Afterwards, the experiments of the deposition of diamond films is performed using the preferred ceramic holder. The diamond coatings on the different positions present a highly uniform distribution on their grain size, thickness, and quality.