The emission spectra of an atom in a cavity for the multiphoton Jaynes–Cummings model are investigated. Using Eberly's formula for the time-dependent physical spectrum, the analytical expression for the atomic emission spectrum is obtained from the two-time dipole-moment correlation function of the atom. The appearance of two strong peaks in the spectrum is explained in detail, and the relationship between the initial photon distributions and the shapes of the spectra are examined. The fundamental differences in the atomic emission spectra for the two-photon and multiphoton models are specified. Furthermore, the role of the detector filter is thoroughly studied. It is explicitly shown that the atomic emission spectra can be obtained by averaging over the convolution integrals between the Fourier transform of the atomic dipole-moment correlation function associated with a pure number state and the detector filter function on frequency domain. The comparisons of the spectra for a coherent initial field to those for a thermal initial field are presented.