In this paper, a novel double Q-switcher structure is designed in order to compensate the thermal induced birefringence in the active medium of 1 kHz laser diode (LD) side-pumped electro-optic Q-switched Nd:YAG laser. The experiment result shows that pulse energy of the double Q-switch Nd:YAG laser is 56% higher than the same situation in single Q-switch uncompensated structure. When the laser output power is up to 450 mJ, pulse energy of 30 mJ is obtained, the extinction ratio of beam is better than 10:1, the pulse duration is about 14 ns, and the optical-to-optical conversion efficiency is 6.7%. At the same time, the novel cavity is modelled and numerically calculating is made by using rate equations, the results are accorded with the experiment.