A SMPS(scanning mobility particle sizer) system measures the number size distribution of particles using electrical mobility detection technique. An aerosol charge neutralizer, which is a component of the SMPS, is a bipolar charger using a radioactive source to apply an equilibrium charge distribution to aerosols of unknown charge distribution. However, the performance of aerosol charge neutralizers is not well known, especially for highly charged particles. In this study, the effect of the particle charging characteristics of two aerosol charge neutralizers on the measurement using a SMPS system was experimentally investigated for highly charged polydisperse particles. One has radioactive source of $^{85}$ Kr (beta source, 2 mCi) and the other has $^{210}$ Po (alpha source, 0.5 mCi). The air flow rate passing through each aerosol charge neutralizer was changed from 0.3 to 3.0 L/min. The results show that the non-equilibrium character in particle charge distribution appears as the air flow rate increases although the particle number concentration is relatively low in the range of 1.5∼2x10$^{6}$ particles/㎤. The low neutralizing efficiency of the $^{85}$ Kr aerosol charge neutralizer for highly charged particles can cause to bring an artifact in the measurement using a SMPS system. However, the performance of the $^{210}$ Po aerosol charge neutralizer is insensitive to the air flow rate.