In a free-space optical communication system with an avalanche photodiode (APD) detector, the average bit error rate (ABER) is studied based on pulse position modulation (PPM) considering Gamma–Gamma atmospheric turbulence and fiber coupling efficiency (FCE). By analyzing the shot noise and thermal noise, the approximate analytical expression of the ABER of binary PPM is theoretically derived. Then, the approximate analytical expression of ABER union bound is derived for L-ary PPM. The FCE has a greater impact on the ABER of the APD detection system than it does on the PIN detection system. By adopting the adaptive optics technology, compared with the PIN detection system, the communication performance of the APD detection is greatly improved. Moreover, the optimal average APD gain of the APD detection system is strongly correlated to the detector temperature but weakly dependent on the atmospheric turbulence intensity, FCE, number of wavefront compensation terms, average received photon number, and receiving aperture size. By optimizing the receiving aperture and designing an accurate temperature control system, the communication performance of the APD detection system can be further improved.