Although extensive studies were conducted for water soluble inorganic ions (WSIIs) in PM2.5, most of them concentrated on developed cities while limited studies in mountainous cities. In this study, daily PM2.5 was sampled for a year (from Sept. 1, 2017 to Aug. 31, 2018) to comprehensively investigate the characteristics of WSIIs in a typical mountainous city, Chongqing. The results showed that air quality in Chongqing was getting better (annual 43.0 μg m−3 PM2.5) but still higher than the NAAQS annual limit. Consistent with PM2.5 pattern, the concentration of WSIIs in dry months with high relative humidity (Nov. 2017–Feb. 2018) was also higher than that in wet months (rest months). The ratio of WSIIs/PM2.5 was similar in dry and wet months, but higher proportion (87.7%) of SNA/WSIIs (SNA: SO42−, NH4+, and NO3−) were found in dry months, suggesting that secondary ions SNA were enriched in dry months. Importantly, the ratio of NO3−/SO42− > 1 in dry months, which was not reported in previous studies, implied that NO3− replaced SO42− and became the predominant pollutant in dry months. Both heterogeneous and homogeneous reactions played important roles in the formation of SO42− and NO3−. Positive matrix factorization further demonstrated that secondary aerosol from coal combustion and agriculture activities (38.5%), secondary aerosol from vehicle exhaust (19.5%), soil dust (13.7%) and industry (28.2%) contributed to WSIIs in Chongqing in 2017–2018. In order to improve air quality in Chongqing, relevant measures should be taken to control the sources of WSIIs.