Direct Lightning strokes to launch pad damage some vital instruments. Thus, the Lightning protection system is used to protect instruments. Calculating the probability of direct Lightning strokes is the main consideration in Lightning protection system design, however this calculation is not simple since the shape of launch pad is complex. In this paper, a 3-D numerical analysis model based on Leader Progression Model (LPM) is proposed to calculate the probability of direct Lightning strokes to launch pads. The progression of Lightning downward leader, the inception and propagation of upward leaders are modeled step by step until final jump. Launch pad, Lightning protection system, downward and upward leaders are modeled by different shapes of charges, and the environment electric field is computed using charge simulation method. Then, Lightning Performance of two actual launch pads are evaluated, and the simulation results are compared. Finally, the high voltage laboratory tests have been achived to validate the proposed protection system design.