A research project of the CFETR Negative ion based Neutral Beam Injection (NNBI) prototype has been started in China. The objectives of the CFETR NNBI protype are to produce a negative hydrogen ion beam of >20 A to 200–400 kV for 3600 s and to attain a neutralization efficiency of >50%. Thus, a neutral beam power of >2 MW is foreseen onto the calorimeter (i.e., beam dump). A gas neutralizer is applied inside the beamline of CFETR NNBI prototype, to achieve the neutralization of negative ion beam through the charge-exchange collisions with the gas target. The most critical issues for the gas neutralizer are to balance the contradictive requirements of high neutralization efficiency, low gas inflow, and low heat load. During the physical design of the neutralizer for CFETR NNBI prototype, two proposals have been considered and studied in detail. One has single beam channel and other one has two narrow channels separated by a panel. The narrow channel design is benefic to decrease gas conductance, and thus reduce the required gas inflow to attain the maximal neutralization efficiency. However, the inserted panel will restrict the extraction area of the beam source, where the aperture columns corresponding to the panel should be masked to avoid the direct beam interception. But the leading edge of the inserted panel will still suffer a high thermal load due to the stray particles from the beam source. A 3D model of the whole beamline of CFETR NNBI prototype has been developed to study the gas flow and the beam transport in the beamline. Based on this model, these two neutralizer designs have been evaluated in detail, in terms of the relation between neutralization efficiency and gas inflow, and the power load on the neutralizer components.