The effect of the wet chemical cleaning process on the surface microroughness of Si wafers was studied, using CZ, FZ, and EPI wafers. It has been shown that the surface microroughness affects the dielectric breakdown characteristics of the oxide: the dielectric breakdown of the oxide degrades as the microroughness of the Si substrate increases. The microroughness on the Si substrate surface and the oxide surface was evaluated with a scanning tunneling microscope (STM) and an atomic force microscope (AFM). The surface microroughness was found to increase in wet chemical processing, in particular in cleaning (APM cleaning). It has been shown that the microroughness does not increase at all if the mixing ratio in solution is suppressed at a low level: (conventional mixing ratio is 1:1:5), and the room temperature ultrapure water rinsing is introduced right after the APM cleaning. At the same time, the APM cleaning with its mixing ratio suppressed at the low level has been found very effective to remove particles and metallic impurities from the Si surface. The increase of microroughness due to the APM cleaning varies among the wafer types; little increase is observed on EPI wafer but significant increase is observed on CZ and FZ wafers. It has been found, however, that the CZ and FZ wafers which go through the wet oxidation at 1000°C for over 4 h, can suppress the increase of microroughness in the APM cleaning at almost the same level as the EPI wafer. This because the interstitial Si atoms generated in the wet oxidation fill the Si vacancy. In the case of the n‐type CZ wafer, the surface microroughness is also observed to increase in the DHF cleaning. It has been revealed the addition of of over 0.5% to the DHF solution can completely suppress this microroughness increase.