A lack of adequate or accepted research methodology has been a major obstacle to study herbal medicines. In this study, instead of the prevalent hyphenated chromatographies, common high performance liquid chromatography equipped with ultraviolet detector (HPLC-UV) and multivariate statistical analysis were utilized to assess the qualities of total flavones of sea buckthorn (TFS), an 85% ethanol extract of the sea buckthorn berries. Two complementary HPLC-UV methods were developed, validated and combined to comprehensively determine the ingredients in TFS. Principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) of the combined analytical data showed that the six batches of TFS could be well differentiated. Hierarchical cluster analysis (HCA) using Ward's minimum variance method of the PLS-DA loading matrix demonstrated the known ingredients (quercetin, kaempferol, isorhamnetin, oleanolic acid and ursolic acid) and three unknown ingredients in TFS significantly contributed to the quality differences. A PLS regression model indicated that the results of the present method correlated well with the content of total flavones, which is now the quality control approach of TFS. Results from this study indicated that the proposed method is reliable for the quality reassessment of some widely used herbal extracts.