An optimal input design method is proposed for online parameter estimation for aircraft with multiple control surfaces. The optimal input is designed considering the input and output constraints. These constraints are constructed based on a military standard, MIL-STD-8785C, viz., the flying qualities of a piloted aircraft. The accuracy of parameter estimation using the optimal input is compared with that of parameter estimation using conventional doublet/3211 inputs. Two online parameter estimation schemes are also considered to evaluate the performance of the designed optimal input: a Bayesian method based on the time domain and an equation-error method based on the frequency domain. The recursive form of the Bayesian method is also derived. Numerical simulations are performed, and the performance, convergence, and accuracy of two online parameter estimation schemes are compared.