The performance of coherent free-space optical (CFSO) communication with phase modulation is limited by both phase fluctuations and intensity scintillations induced by atmospheric turbulence. To improve the system performance, one effective way is to use digital phase estimation. In this paper, a CFSO communication system with quadrature phase-shift keying modulation is studied. With consideration of the effects of log-normal amplitude fluctuations and Gauss phase fluctuations, a two-stage Mth power carrier phase estimation (CPE) scheme is proposed. The simulation results show that the phase noise can be suppressed greatly by this scheme, and the system symbol error rate performance with the two-stage Mth power CPE can be three orders lower than that of the single-stage Mth power CPE. Therefore, the two-stage CPE we proposed can contribute to the performance improvements of the CFSO communication system and has determinate guidance sense to its actual application.