Inorganic or organic acid pollution gases in the ambient air of museums can corrode brick and stone cultural relics in the collection and cause harmful salts to be deposited on their surfaces. Common harmful salts have complex types and may contain both inorganic and organic acid anions. In order to further understand the salt damage to cultural relics and to analyze its causes, we developed a method for quantitatively analyzing inorganic and organic anions in harmful salts based on ion chromatography. This method can simultaneously determine 12 anions—fluoride, chloride, bromide, nitrate, nitrite, phosphate, sulfate, formate, acetate, propionate, butyrate and valerate—in harmful salts found on brick and stone cultural relics in the collection. With a gradient of 2~30 mmol/L KOH, the separation and accurate detection of the 12 anions could be achieved in 35 min. The correlation coefficients of their standard curves were higher than 0.995, the detection limits 0.001~0.022 μg/mL, the quantitation limits 0.004~0.073 μg/mL and the recovery rates 81.8%~107.0%. The solvent for this method was ultrapure water, and the sample was easy to handle. This method features low cost, short detection time and high accuracy. The mass fractions of inorganic and organic acid anions in harmful salts can be calculated quantitatively. This method was applied to the analysis of salt damage on the surfaces of a tile and an imitation censer in the collection of the National Museum of China, and suggests the types of environmental pollutants that led to the precipitation of harmful salts. This work provides a basis for preventing, delaying and predicting the occurrence of salt damage, as well as analyzing its causes.