Abstract. Atmospheric cluster ions are important constituents in the atmosphere, and their concentrations and compositions govern their role in atmospheric chemistry. However, there is currently limited quantitative research on atmospheric ion compositions, sources, and sinks, especially in the urban atmosphere where pollution levels and human populations are intense. In this study, we measured the compositions of negative cluster ions and neutral molecules using an atmospheric pressure interface high-resolution time-of-flight mass spectrometer (APi-TOF) and a chemical ionization mass spectrometer in urban Beijing. Quantitative analysis of cluster ions was performed by their comparison with condensation sink (CS), reagent ions, and neutral molecules. We demonstrate the feasibility of quantifying cluster ions with different compositions using in situ-measured ion mobility distributions from a neutral cluster and air ion spectrometer (NAIS). The median concentration of negative cluster ions was 85 (61–112 for 25 %–75 %) cm−3 during the measurement period, which was negatively correlated with CS. The negative cluster ions mainly consisted of inorganic nitrogen-containing ions, inorganic sulfur-containing ions, and organic ions in the form of adducts with NO3- or HSO4-. The CHON-related organic ions accounted for over 70 % of the total organic ions. Although the molecules clustered with NO3- and HSO4- had similar compositions, we found that HSO4- clustered more efficiently with CHO and CHONnonNPs species (CHON excluding nitrated phenols), while NO3- clustered more efficiently with nitrated phenols (CHONNPs). Additionally, most organic ions were positively correlated with neutral molecules, resulting in similar diurnal cycles of organic ions and neutral molecules. However, an exception was found for CHONNPs, the concentration of which is also significantly influenced by the reagent ions NO3-. The charge fractions are generally higher for molecules with higher molecular weight and a higher oxidation state, and the opposite diurnal variations in charging fractions between H2SO4 and organic species indicate a charging competition between them. Finally, we choose HSO4- and C3H3O4- as representatives to calculate the contribution of different formation and loss pathways. We found their losses are condensational loss onto aerosol particles (73 %–75 %), ion–molecule reaction losses (19 %), and ion–ion recombination losses (6 %–8 %).