In order to realize online trajectory optimization for midcourse guidance of the near space interceptor, an online trajectory generation algorithm is designed based on the neighboring optimal control(NOC) theory and improved indirect Gauss pseudospectral method(GPM). A trajectory optimization model is designed according to the features of operation in the near space. The two points boundary value problem is deduced based on the NOC theory.The transversality conditions are further differentiated to second order and the optimal co-state modifications are expressed in terms of current state derivations and terminal constraint modifications by backward recursion. By treating the current states and the optimal co-state modifications as initial constraints and perturbations, the feedback control variables are obtained based on the improved indirect GPM and nominal trajectory information. The simulation results show that this method can generate a modified trajectory effectively with high precision of terminal modifications.