The frequency of 1090 MHz is generally used in aviation systems. These signals with the same frequencies may superpose over the time. The distribution of signal characteristic values over the time is used to determine the superposing situation of signals, and then Projection Algorithm (PA) is used to separate the superposed signals. A simulation model was established by using the toolbox of Matlab Simulink for 1090 MHz signal separation, and expected results were obtained. The simulation results show that projection algorithm can effectively separate two superposed S mode signals, which is also adaptable for A/C mode signals.