Using ray-matrix method we investigated the resonators containing two kinds of apertures. For the first one with soft-aperture, a general analysis solution of eigenmodes was derived on the basis of the diffraction integral equation. The relationship between the features of the zero-order mode and size and position of the aperture was investigated. For the second one with hard-aperture, we substituted a Gaussian aperture with suitable diameter for the used aperture, the approximate solution of eigenmode was obtained. The result was used for analysing the mode-selecting resonator with iris, the self-aperture mode-selecting resonator and thermo-insensitive resonator containing a aperture. The theory has been well verified by our experiments.