The flight controller should meet the flying qualities, stability margins, and time response requirement according to the class of a target aircraft or UAV. Classical design process of PID controller is a very time consuming process and needed trial and erros. The best way is to apply the multi-disciplinary optimization algorithm to meet the numerous constraints of controller requirements. This paper presents how multi-objective parameter optimization (CONDUIT) can be used to determine many design parameters of lateral stability and augmentation system for roll and heading controller of the small UAV. To verify the effectiveness of applying the optimization method, designed controller using optimization are compared with the baseline controller that is designed only considering the time responses.