In this paper, we investigate that the effects of weather, exponentiated Weibull turbulence and generalized pointing errors based on Beckmann distribution on partially coherent beams and establish a joint channel statistical model, then derive new expressions of the performance parameters of free space optical communication system based on On-Off keying (OOK) modulation by using Meijer's-G function and Fox-H function, such as average bit error rate (BER), average channel capacity and outage probability. For an atmospheric laser communication system with 1550 nm wavelength and 1 km terrestrial level link, the performance parameters of the system are simulated and analyzed. The results show that with the increase of signal to noise ratio (SNR), the compensation effect for strong turbulence becomes more obvious; on the premise of sacrificing less channel capacity, reducing the spatial coherence length or increasing the plane spot size of the transmitter can significantly improve the BER and outage probability performance of the system; with the increase of receiver aperture diameter, the aperture average effect is more obvious; increasing the receiver aperture diameter can significantly improve the overall performance of the system; in the design of APT (Acquisition,Pointing and Tracking) subsystem, when a certain boresight error is allowed, the random jitter of transmitter is reduced as much as possible.