Performance comparison between a custom-made soft X-ray neutralizer (CM-SXR) and a commercial counterpart (TSI-SXR, advanced aerosol neutralizer, model 3088, TSI, USA) is made by using a scanning mobility particle sizer (SMPS). The results show that for all the tested particles (i.e., Polystyrene latex particles, ammonium sulfate particles, sodium chloride particles, and room air particles) with a size greater than 20 nm, the particle number concentration measured by CM-SXR is higher than that measured by TSI-SXR when the differential mobility analyzer (DMA) is operated under the negatively-charged particle mode, and the differences can be up to 40%. However, opposite results have been found when the DMA is operated at the positively-charged mode, that is the particle number concentration measured by TSI-SXR is higher than that measured by CM-SXR and the differences are up to 77%. Possible reasons accounting for the above differences are discussed, and it is deduced that the mounting position of the soft X-ray in the two neutralizers, which results in different exposures of the X-ray and the differences of the residence time when the sample passes the two different neutralizers, is likely the main reason leading to different positively-and negatively-charged particle distribution inside the neutralizers.