Satellite-based global quantum secure communication is the challenge of telecommunication. It is necessary to face the interaction between infrared wave and the atmosphere. In this letter, we study the atmospheric attenuation and turbulent effect on a low earth orbit satellite quantum communication system at 0.8 μm. By numerical analyzing the atmospheric attenuation between earth-based station and low earth orbit satellite, it is shown that, when the visibility is below 5 km, atmospheric attenuation is obvious on earth-satellite path. Calculation of effect of turbulent atmosphere on infrared wave is shown that, the atmospheric attenuation from low earth orbit satellite to earth based station is about 6dB when clear condition. By applying the quantum computation language which is used in quantum computation to the research of quantum communication, simulation experiment of a secure communication protocol is achieved. The results of the simulation experiment were tallied with numerical ones, which verified the feasibility of the low earth orbit satellite quantum communication system.