A method of beam alignment detection is proposed for the acquisition, pointing and tracking system in atmospheric laser communication based on extension of beam propagating in atmospheric turbulence, back projection imaging principle and Cassegrain telescoping system. The method is analyzed theoretically and verified experimentally. Based on the shape and centroid of the beam spot, the transverse deviation and the axial deflection of the beams are calculated comprehensively. As a result, the problems with the general method are solved, one of which is that the beam spot fluctuation is caused by transverse displacement or axial displacement, and another is that the transverse displacement can not be calculated by the general method. The experimental results show that the method can detect effectively the beam alignment state, and realize finally resolution ratio with 2.2 μrad in axial deflection and 0.25 mm in transverse deviation.