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A simple and reliable method of ultra-performance liquid chromatography with photodiode array detector (UPLC-PDA) was developed to control the quality of <em>Radix Isatidis</em> (dried root of <em>Isatis indigotica</em>) for chemical fingerprint analysis and quantitative analysis of eight bioactive constituents, including <em>R</em>,<em>S</em>-goitrin, progoitrin, epiprogoitrin, gluconapin, adenosine, uridine, guanosine, and hypoxanthine. In quantitative analysis, the eight components showed good regression (<em>R</em><em> </em>> 0.9997) within test ranges, and the recovery method ranged from 99.5% to 103.0%. The UPLC fingerprints of the <em>Radix Isatidis </em>samples were compared by performing chemometric procedures, including similarity analysis, hierarchical clustering analysis, and principal component analysis. The chemometric procedures classified <em>Radix Isatidis</em> and its finished products such that all samples could be successfully grouped according to crude herbs, prepared slices, and adulterant <em>Baphicacanthis cusiae</em> Rhizoma et Radix. The combination of quantitative and chromatographic fingerprint analysis can be used for the quality assessment of <em>Radix Isatidis</em><em> </em>and its finished products.