An improved ion chromatographic method including two elution procedures was proposed for the quantitative determination of atmospheric alkylamines in field atmospheric samples involving high levels of inorganic cations by using 18-crown-6 as mobile phase additive. When 18-crown-6 was added to the mobile phase, the retention times increased significantly for Na+, NH4+, K+ and primary alkylamines but decreased for secondary and tertiary alkylamines due to the complexation with certain cations and interaction with both stationary and mobile phases of 18-crown-6. As a result, the separation of the cations was greatly promoted, which reduced the interference of peak distortion of overloaded inorganic cations on the quantitation of adjacent alkylamines. By using the presented method, five inorganic cations (Na+, NH4+, K+, Mg2+, Ca2+) and six alkylamines (dimethylamine (DMAH+), trimethylamine + diethylamine (TMAH+ + DEAH+), propylamine (MPAH+), triethylamine (TEAH+), ethanolamine (MEOAH+) and triethanolamine (TEOAH+)) were effectively separated and determined, and the relative standard derivations (RSDs) of objective cations were all less than 1% for retention time and 3.1% for peak area (n = 9), respectively. The linearity was excellent for each cation (R2 > 0.993) except for NH4+ and TEOAH+ showing a non-linear response (R2 > 0.998 for theoretical non-linear fitting), and the detection limit of these cations were 0.03–1.19 ng. The proposed method was successfully used in the determination of both alkylamines and inorganic cations in ambient particulate matters and gaseous alkylamines in ceiling duct exhaust. The annual average concentrations of DMAH+, TMAH+ + DEAH+ and TEAH+ were 15.56, 4.35 and 16.00 ng m−3 in PM2.5 over Shanghai in 2013. The concentrations of gaseous DMA and TMA + DEA in ceiling duct exhaust reached a maximum of 940.0 and 112.7 μg m−3, and were positively correlated with the human activity intensity, suggesting that human excreta emissions was a potential important source of atmospheric alkylamines in urban area of Shanghai.