Thermophoresis of charged colloids in aqueous media has wide applications in biology. Most existing studies of thermophoresis focused on spherical particles, but biological compounds are usually non-spherical. The present paper reports a numerical analysis of the thermophoresis of a charged spheroidal colloid in aqueous media. The model accounts for the strongly coupled temperature field, the flow field, the electric potential field, and the ion concentration field. Numerical simulations revealed that prolate spheroids move faster than spherical particles, and oblate spheroids move slower than spherical particles. For the arbitrary electric double layer (EDL) thickness, the thermodiffusion coefficient of prolate (oblate) spheroids increases (decreases) with the increasing particle’s dimension ratio between the major and minor semiaxes. For the extremely thin EDL case, the hydrodynamic effect is significant, and the thermodiffusion coefficient for prolate (oblate) spheroids converges to a fixed value with the increasing particle’s dimension ratio. For the extremely thick EDL case, the particle curvature’s effect also becomes important, and the increasing (decreasing) rate of thermodiffusion coefficient for prolate (oblate) spheroids is reduced slightly.