Through the monitoring of geochemical indexes in underground river of Xueyu Cave in Chongqing under rainfall conditions, we found that all indexes responded quickly to rainfall, and there was a correlation among them. Each index was analyzed with the principal component analysis, three main components were extracted which can represent 82.761% of the information to reflect the formation of geochemistry in underground river under rainfall conditions. The results showed that the contribution rates of soil leaching represented as increased concentration of total Fe, total Mn, and Al3+, and dilution effect represented as reduced concentration of K+, Na+ and Sr2+ to the change of geochemical characteristics were 41.718%, which should be paid more attentions for its great damage to karst soil and safety of drinking water. Karst water dissolution of dolomite and recharge area of agricultural activities, caverns were 29.958%, as for karst water on limestone dissolution represented, as increased concentration of Ca2+ the contribution rate was 11.084%.