Photon counting imaging system has recently received a lot of attention in ultra-weak light detection. It has high sensitivity and temporal resolution. The single-point scanning photon counting imaging system typically accumulates a large number of photon events to reconstruct depth image. Acquisition time is redundant or insufficient, which limits imaging efficiency. In this work, a new method called adaptive acquisition time scanning method (AATSM) is proposed to solve this dilemma. Comparing with the fixed acquisition time of every pixel, the method can automatically select the acquisition time of per pixel to reduce total time of data collecting while obtaining depth images. In experiment, we acquire the depth images with the same quality by different scanning methods, showing the feasibility of AATSM. The total time of collecting data by the AATSM can be reduced to 11.87%, compared with fixed acquisition time of every pixel. This demonstrates the capability of speed scanning of AATSM, which can be used for the fast imaging of photon counting system.