Differential phase shift keying (DPSK) modulation and multi-aperture receiving are effective means for suppressing flickering, deviation, and fragmentation of the light spot by atmospheric turbulence. What is challenging in coherent beam combination of such an array receiver system is to detect and compensate for phase deviation of sub-apertures. In this paper, a method of phase alignment of an array optical telescope system using balanced detection was proposed and demonstrated. The improved Mach Zehnder Interferometer (MZI) can demodulate the digital signal and recover the phase difference at the same time. It also brings a 3 dB gain to the receiver and improves the detection sensitivity of the system. Adequate simulations with OptiSystem and MATLAB were carried out to show that the power value remains near the ideal state of 2.75 mW, and the bit error rate is less than 10−9 after phase compensation, which indicates the effectiveness and accuracy of the proposed method. Furthermore, taking the communication interruption difference of ninety degrees as an example, the system bit error rate was reduced from 1 to 10−35, and communication was established again.