The background cold electron density plays an important role in plasma and wave dynamics. Here, we investigate an event with clear modulation of the particle fluxes and wave intensities by background electron density irregularities based on Van Allen Probes observations. The energies at the peak fluxes of protons and Helium ions of 100 eV to several keV are well correlated with the total electron density variation. Intense electromagnetic ion cyclotron (EMIC) and magnetosonic (MS) waves are simultaneously observed in the high‐density regions and disappear in low‐density regions. Based on the linear theory of wave growth, the EMIC waves are generated by the ~10 keV protons, while most MS waves are generated by the positive gradient of proton phase space density at several hundred eV in the high‐density regions. Our results indicate the importance of background plasma density structures in generation of plasma waves by unstable ion distributions. Plain Language Summary The background electron density decreases away from the Earth with a sharp boundary in the density profile, which is defined as the plasmapause. Density irregularities are frequently observed near the plasmapause, and these density structures are believed to play an important role in the generation and propagation of plasma waves. In this letter, we report an event with clear modulation of particle fluxes and electromagnetic ion cyclotron (EMIC), MS as well as the electrostatic waves by the background plasma density structure at a plasmapause crossing near the postdusk magnetic equator based on Van Allen Probe B observation on 9 October 2013. It is shown that the energies of peak fluxes for proton and helium suprathermal populations are well correlated with the background electron density variations. In addition, EMIC and MS waves are simultaneously observed in high plasma density regions but vanish in low‐density regions. Furthermore, the broadband electrostatic waves occur in the density depletion regions. Our simulations indicate that the variations of electromagnetic waves are caused by the wave generation conditions in association with the density irregularities. Key Points Van Allen Probe B observed an electron density structure near the plasmaspheric plume region at the postdusk sector The suprathermal ion fluxes were modulated by the electron density structure showing evidence of transverse ion heating EMIC and MS waves were simultaneously observed in the high‐density regions while electrostatic waves were present in the low‐density regions