In measurement-device-independent quantum key distribution (MDI QKD), the setup of Bell state measurement (BSM) usually requires that the photons sent by different users should be frequency degenerate. It increases the complexity to implement MDI QKD since a complicated feedback system is usually required to calibrate photons’ frequencies in different users. It also limits the development of MDI QKD networks since wavelength division multiplexing (WDM) technology is not compatible with this requirement. In this work, we propose a MDI QKD scheme of frequency-nondegenerate photons, in which the users send photons with different frequencies. It is based on a BSM setup with a frequency-domain beam splitter (FBS), which is realized by a phase modulator (PM). A proof-of-principle experiment is realized, showing that the BSM of frequency-nondegenerate photons could select specific users to realize MDI QKD by adjusting the modulation frequency of the PM to match the frequency difference of photons sent by the users. The results manifest that our scheme has great potential for simplifying the implementation and realizing MDI QKD networks combined with WDM.