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A systematic method for nonlinear analysis, design, and estimation in the frequency domain is proposed in this study using a new concept---nonlinear characteristic output spectrum (nCOS). The nCOS function is an analytical and explicit expression for the relationship between nonlinear output spectrum and system characteristic parameters of interest (including frequency, nonlinear parameters, and excitation magnitude), and can provide a significant insight into nonlinear analysis and design in the frequency domain. Given some simulation or experimental output data of a nonlinear system, the nCOS function of the system can be accurately determined up to any high nonlinear orders with less simulation trials and computation cost compared with a pure simulation-based study or traditional theoretical computations. Moreover, the method can also be used to accurately determine the linear and nonlinear components in the nonlinear output frequency response (or an output spectrum) of a nonlinear system. These results are definitely of significance to nonlinear analysis and design, nonlinear signal processing, system identification, fault detection, etc., in practice. Examples and case studies including analysis of a nonlinear vehicle suspension system are given to illustrate the results.