The time–frequency domain decomposition technique has been proposed for modal identification in ambient vibration testing. In the presence of harmonic excitations, the modal identification process can provide not only structural modes but also non-structural ones relative to harmonic components. It is thus important to distinguish between them. In this study, by using the time–frequency domain decomposition technique, it is demonstrated that the distinction between non-structural harmonic components and those of the structural responses can be possible, and it is merged into the general procedure of the time–frequency domain decomposition method. This proposition is then verified by numerical examples and by a laboratory test.