The 532 nm Doppler lidar developed by the National Space Science Center, Chinese Academy of Sciences, is mainly used to measure the atmospheric wind field, temperature, and density. Maintaining a same reference frequency is a key technology to ensure the normal operation of the Doppler lidar. This lidar system uses seed injection technique to obtain a single mode pulse laser, and maintains the same reference frequency by locking the seed laser into the iodine absorption line. The frequency of the seed laser can be adjusted by two mechanisms: applying a voltage to a piezoelectric(PZT) crystal or changing the temperature of the laser crystal. The response speed of the two kinds of tuning mechanism is different. PZT tuning has a fast response speed but a narrow tuning range, while the thermal tuning has a wide tuning range and a low response speed. A long-term frequency stabilization system was designed by coordinating the two kinds of frequency tuning mechanism. And a Proportion Integration Differentiation(PID) algorithm was used to calculate the feedback voltage. The system did not require a acquisition card with a large range of output voltage. In this system, the laser frequency drift in long term and large range will be tuned by thermal tuning mechanism, while the instantaneous frequency drift will be responded by PZT tuning. The accuracy of the new frequency stabilization system is 350 kHz. The system can work well as long as twenty hours.