A method by low speed pre-acquiring and high speed accurate addressing of reference speckle acquisition is proposed to solve the limit of the low acquisition speed of reference arm array CCD. According to the method, an experimental system of prebuilt three-dimensional ghost imaging lidar is established. In order to ensure the twice sampling independence of preset trajectory scheme using the speckle size decided by translating a system once. The correlation of the speckle field is used as the evaluation function. Experimental results show that the programming is precise and repeatable. Meantime, an experiment with prebuilt three-dimensional ghost imaging lidar in 2 kHz acquisition speed is performed, and the results are almost same as the real-time acquired three-dimensional ghost imaging lidar with the real-time sampling rate of 100 Hz, which demonstrates the effectiveness of this method.