Thermal depolarization caused by birefringence is a major factor that limits the output power of linearly polarized Nd:YAG laser. This paper theoretically analyzes the thermal depolarization of [111]- and [100]-cut Nd:YAG rods and output power of two diode-pumped Nd:YAG rods are compared experimentally. 3×80 mm sized [111]- and [100]- cut rods with doping concentration of 1.1±0.1at.% are used. With a pump power of 180 W, the ratio of linearly polarized output power versus unpolarized output power obtained with the [111]- and [100]- cut rods are 19% and 43% respectively, with a difference of 24%. The experiment demonstrates that in comparison with conventional [111]- cut Nd:YAG rod, [100]- cut Nd:YAG rod can improve the linearly polarized output power obviously. The thermal depolarization depends on the polarization direction for the [100]- cut Nd:YAG rod, and the linearly polarized output power can be improved by suitably modification of the polarization direction of linearly polarized laser to minimize thermal depolarization.