Bit error rate (BER) is an important evaluation index of free space optical communication (FSO), and how to exactly get the BER statistics is rather important. We study the technique of analyzing the BER of FSO based on Monte Carlo simulation using Matlab software. The FSO system and the principle of Monte Carlo simulation are introduced. The method of getting the BER statistics is researched, and the method of generating information source, the channel model, and the calculation of signal-to-noise ratio (SNR) parameter for simulation are given detailedly. Moreover, part of the core Matlab program is presented. The modeling and simulation based on the low-density parity check (LDPC) code and pulse position modulation (PPM) are implementted. The analysis results under different conditions of weather and signal-to-noise ratio indicate the this method is accurate and pratical.