The invention provides a high-precision three-dimensional imaging device based on Geiger APD arrays and a using method thereof. A transmitting objective lens, a light splitter mirror and an interference filter are sequentially arranged in front of an optical axis of the three-dimensional imaging device. An optical fiber bundle, the Geiger APD arrays and a system control unit are arranged on the rear portion of the optical axis of the three-dimensional imaging device, and the output ends of the Geiger APD arrays are connected with the system control unit. A high-frequency laser is arranged on the side portion of the light splitter mirror. According to the high-precision three-dimensional imaging device, the high-precision image resolution is achieved through matching of the core diameter of an optical fiber and the focal length of the objective lens. Meanwhile, a plurality of small-scale Geiger APD arrays are coupled together through optical fiber beams to achieve staring three-dimensional imaging, and the defect that the imaging frequency is low due to small-scale Geiger APD array scanning imaging is overcome. The detecting area of all units of the Geiger APD arrays is large, and complete matching of a micro lens array focus plane and the Geiger APD arrays can be guaranteed by adjusting optical fiber intervals in the optical fiber beams.