For the application of laser detection over a long distance of 100 km, to achieve the long-distance detection, the system mostly uses low repetition frequency, high pulse energy laser and large diameter telescope, which leads the shortcomings of large volume, heavy weight and high power consumption. The lidar based on photon counting technology has the characteristic of high sensitivity. It greatly reduces the laser energy and receiving telescope aperture of the system. The volume, weight and power consumption of the system are reduced. A kind of laser ranging lidar applied in high-altitude remote detection of small target is designed, which adopts Geiger-mode avalanche photo diode achieving photon counting, and realizes the miniaturization of the system. The system design principle, component, and the experiment result are introduced in detail. The results show that when the round-trip atmospheric transmittance is 0.25, the maximum detection range can reach 100 km for the small target with 6 m2 effective reflection area and 0.1 reflectivity, and the range resolution is 6 m.