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Free space optical(FSO) communication can provide high bandwidth, high security communication services. it is attractive for its convenient establish the communication link and low power consuming. As the active received area of optical fiber is very small, when using optical fiber technology in FSO system, we must consider the effects of angle of arrival. Tracking subsystem is an effective method to mitigate the effects of turbulence. Using tracking system FSO demonstration, We found that when the turbulence is strong, the received power intensity fluctuation is very large. This is because when the turbulence is strong, the tracking error tracking subsystem increased a lot; therefore sometime the tracking system cannot focus the optical signal into the fiber. The bit error rate of communication system increase a lot. Time diversity is a useful technology for the time varied channel. We use theoretical analysis and did numerical simulations on the new scheme of time diversity FSO system with tracking antenna; The independent time interval of the system is also discussed. we found the new scheme can improve the throughput performance of conventional FSO system.