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A modified Hong–Ou–Mandel (HOM) interference reveals that the two-photon interference phenomenon can be explained only by the concept of a two-photon wave packet rather than a single-photon one. However, the temporal interferogram in the modified HOM interferometer becomes flat in some cases so that no useful information can be extracted from time-domain measurement. Here, we theoretically explore such temporal interferogram from the frequency domain and obtain the spectrally resolved interference with high visibility. The result represents a modulation of the joint spectral intensity along both the frequency sum and the frequency difference directions. This is quite different from the cases of the spectrally resolved HOM interference and N00N state interference where the modulations happened only in one direction. Moreover, we have shown that such modulations have a potential application in the generation and characterization of high-dimensional frequency entanglement. • Spectrally resolved interference with high visibility in the modified HOM interferometer can be obtained even if the temporal visibility is zero. • Joint spectral intensity can be modulated by the time delay along both the frequency sum and the frequency difference directions. • High-dimensional frequency entanglement can be generated by adjusting the time delay and can be characterized directly using the two-side dips appeared in temporal interferogram. • The research results could facilitate further development of spectrally resolved multi-photon interference and its applications in quantum information science. [ABSTRACT FROM AUTHOR]