The free space optical (FSO) communication system has attracted many researchers from different countries, owning to its advantages such as high security, high speed and anti-interference. Among all kinds of the channels of the FSO communication system, the atmosphere channel is very difficult to deal with for two typical disadvantages at least. The one is the scintillation of the optical carrier intensity caused by the atmosphere turbulence and the other is the multipath effect by the optical scattering. A lot of studies have shown that the MIMO (Multiple Input Multiple Output) technology can overcome the scintillation of the optical carrier through the atmosphere effectively. So the background of this paper is a MIMO system which includes multiple optical transmitting antennas and multiple optical receiving antennas. A number of particles such as hazes, water droplets and aerosols exit in the atmosphere widely. When optical carrier meets these particles, the scattering phenomenon is inevitable, which leads to the multipath effect. As a result, a optical pulse transmitted by the optical transmitter becomes wider, to some extent, when it gets to the optical receiver due to the multipath effect. If the information transmission rate is quite low, there is less relationship between the multipath effect and the bit error rate (BER) of the communication system. Once the information transmission rate increases to a high level, the multipath effect will produce the problem called inter symbol inference (ISI) seriously and the bit error rate will increase severely. In order to take the advantage of the FSO communication system, the inter symbol inference problem must be solved. So it is necessary to use the channel equalization technology. This paper aims at deciding a equalizer and designing suitable equalization algorithm for a MIMO free space optical communication system to overcome the serious problem of bit error rate. The reliability and the efficiency of communication are two important indexes. For a MIMO communication system, there are two typical equalization methods. The first method, every receiving antenna has an independent equalizer without the information derived from the other receiving antennas. The second, the information derived from all of the receiving antennas mixes with each other, according to some definite rules, which is called space-time equalization. The former is discussed in this paper. The equalization algorithm concludes training mode and non training mode. The training mode needs training codes transmitted by the transmitter during the whole communication process and this mode reduces the communication efficiency more or less. In order to improve the communication efficiency, the blind equalization algorithm, a non training mode, is used to solve the parameter of the equalizer. In this paper, firstly, the atmosphere channel is described focusing on the scintillation and multipath effect of the optical carrier. Then, the structure of a equalizer of MIMO free space optical communication system is introduced. In the next part of this paper, the principle of the blind equalization algorithm is introduced. In addition, the simulation results are showed. In the end of this paper, the conclusions and the future work are discussed.