In order to improve the performance of free space optical communication system with multiple apertures transmitting, based on the "Research and verification of key technologies of marine high speed communication network" project, an analytical expression of bit error rate(BER) is proposed. The communication system uses intensity-modulation with direct-detection (IMDD) and works in a turbulent environment described by exponentiated Weibull(EW) distribution model. The aperture averaging effect under different channel parameters and the impacts on the average BER with different transmitting aperture numbers and communication rates are analyzed. The simulation results show that the multiple apertures transmitting system has good turbulence suppression ability at low communication rate. The difference of arrival time caused by different transmitting apertures will increase the bit error probability of the communication system at high communication rate.