Considering the disturbance of the plasma electrons at the beam-ion channel boundary, the eigen-equation of TM mode has been derived. On the basis of comparing the electromagnetic characteristics of the beam-ion channel with a traditional medium waveguide for the condition of a step-boundary defined in this paper, the numerical simulation results show that by changing the plasma frequency one can control the electromagnetic working mode in ion channel. Analyzing the influence of the disturbed charge boundary and the step-boundary on electromagnetic mode in the beam-ion channel, one can find that the cut-off frequency of the beam-ion channel have increased in the low frequency range effectively (ωωp， ωp is the plasma frequency) and some new electromagnetic modes appear in the high frequency range (ω>ωp) with the disturbed charge boundary. These findings can provide an important theoretical basis for the design of the ion channel electronics cyclotron maser (ICECM) and the ion channel laser (ICL).