In order to analyze a microwave neutralizer in ion’s time/space scales, a three-dimensional Hybrid-PIC (Particle-In-Cell) solver which treats ions and electrons as particles and fluid was developed. In this analysis, microwave power absorption distribution was estimated by means of another electromagnetic PIC solver. The results show that qualitative agreement on voltage-current characteristics was achieved, whereas a discontinuous current jump between a low current mode and a high current mode was still diffused. It is found that, in the high current mode, the electric potential is gradually increased toward the plume region inside the orifice, which promotes high ion production rate there. It is also shown that the sputtering rate of an antenna is comparable with the measured data, where doubly-ionized ions mainly produced inside the orifice considerably aggravate the sputtering rate.