A set of three wavelength Nd:YAG laser system with high stability and high energy output is designed, which is used as laser cleaning source. The system includes an oscillator, an amplifier and subsequent wavelength switching system. In order to solve the output energy decreasing and instability caused by thermal birefringence effect of the laser rod, a quarter wave plate is inserted between the output mirror and laser medium, and the compensation effects of the waveplate are investigated. Results show that output energy of the oscillator increases by 10% and the stability is improved obviously after inserting the waveplate. When the repetition frequency is 10 Hz, the single pulse energy of 1064 nm laser after amplificating reaches 700 mJ. It passes through the frequency doubling crystal BBO, and 325.6 mJ single pulse energy of 532 nm laser is obtained. The single pulse energy of 266 nm laser is 84 mJ after fourth harmonic generation. Three wavelength laser output energy instability is less than 0.6% in one hour.