In order to solve initial alignment of antenna for laser communication system between an aircraft and a ground station,the composition and algorithm theory of an antenna alignment system were demonstrated in detail,and the experimental data were analyzed.The parameters of position and attitude of communication terminals were obtained using GPS,INS and etc,the azimuth and elevation essential to antenna alignment of two terminals were obtained by coordinate conversion.By doing an experiment between two pots of 12.5 km distances,the data of initial alignment of antenna were given,and the initial alignment of antenna was completed.Experiment shows the area of uncertainty is 35 mrad,which will be the foundation of antenna scanning.