This paper deals with supersonic air-breathing missile system. A supersonic air-breathing missile system has very complicated and incoherent thrust characteristics with respect to outer and inner environment during operation. For this reason, the missile system has many maneuver constraints and is allowed to operate within narrow flight envelope. In this paper, trajectory optimization of the missile is accomplished. The trajectory optimization problem is formulated as a discrete parameter optimization problem. For this formulation, Legendre Pseudo-Spectral method is introduced. This method is based on calculating the state and control variables on Legendre-Gauss-Lobatto (LGL) points. This approach helps to find approximated derivative and integration quantities simply. It is shown that, for this trajectory optimization, trend analysis is performed from thrust characteristics on various conditions so that the trajectory optimization is accomplished with fine initial guess with these results.