In this paper, we compared and analyzed 3D silicon-oxide-nitride-oxide-silicon (SONOS) multi layer flash memory devices fabricated on nitride or oxide layer, respectively. The device fabricated on nitride layer has inferior electrical properties than that fabricated on oxide layer. However, the device on nitride layer has faster program/erase speed (P/E speed) than that on the oxide layer, although having inferior electrical performance. Afterwards, to find out the reason why the device on nitride has faster P/E speed, 1/f noise analysis of both devices is investigated. From gate bias dependance, both devices follow the mobility fluctuation model which results from the lattice scattering and defects in the channel layer. In addition, the device on nitride with better memory characteristics has higher normalized drain current noise power spectral density (S(ID)/I(D)2), which means that it has more traps and defects in the channel layer. The apparent hooge`s noise parameter (αapp) to represent the grain boundary trap density and the height of grain boundary potential barrier is considered. The device on nitride has higher αapp values, which can be explained due to more grain boundary traps. Therefore, the reason why the devices on nitride and oxide have a different P/E speed can be explained due to the trapping/de-trapping of free carriers into more grain boundary trap sites in channel layer.