The adverse effects of acidic ultrafine particles (AUFPs) have been widely recognized in scientific communities. However, a handful of studies successfully acquired the concentrations of AUFPs in the atmosphere. To explore the AUFPs pollution, six extensive measurements were for the first time conducted in the roadside, urban and rural areas in Hong Kong, and the urban area in Shanghai between 2017 and 2020. The concentrations of AUFPs and UFPs, and the proportions of AUFPs in UFPs were obtained. The concentration of UFPs was the highest at the roadside site, followed by the urban site and the rural site, while the proportion of AUFPs in UFPs showed a contrary trend. The difference, on one hand, indicated the potential transformation of AUFPs from non-acidic UFPs during the transport and aging of air masses, and on the other hand, suggested the minor contribution of anthropogenic sources to the emission of AUFPs. In addition, the urban area in Hong Kong suffered from heavier pollution of UFPs and AUFPs than that in Shanghai. As for size distribution, the proportion of AUFPs in UFPs peaked in the size range of 35–50 nm and 50–75 nm in roadside and urban area, respectively. In rural area, the peak was observed in the size range of 5–10 nm, which might indicate the stimulation of new particle formation with the AUFPs as seeds. Furthermore, in the urban areas of Hong Kong and Shanghai, no significant difference was found for the geometric mean diameters of UFPs and AUFPs (p > 0.05). At last, the sulfuric acid proxy was positively correlated with the proportions of AUFPs in UFPs but not well correlated with the AUFPs levels. The results suggested the important roles of interaction between sulfuric acid vapor and non-acidic UFPs in AUFPs formation. Due to the significant reduction of sulfur dioxide in China during the last decade, the pollution of AUFPs in urban areas was alleviated.