A high-performance liquid chromatography method with diode array detection was developed for simultaneous analysis of organic acids (chlorogenic acid, caffeic acid, 4,5-dicaffeoylquinic acid) and flavonoids (baicalin, baicalein, wogonin) in Shuang-huang-lian injection, a traditional Chinese medicine being prescribed widely for anti-bacterial, anti-viral and immunostimulant activity. All calibration curves showed good linear correlation (r(2) > 0.9997) within the test ranges. Validation proved that the repeatability of the method was good and recovery was satisfactory. The validated method was successfully applied to 24 batches of Shuang-huang-lian injection. The result showed that there was a great variation among different samples. Principal component analysis further proved considerable variations among the samples from eight manufacturers, and suggested that chlorogenic acid and baicalin might have the greatest variations among the 24 batches. In conclusion, these results demonstrated that the method proposed was very useful for the analysis and quality consistency evaluation of Shuang-huang-lian injection.