A simple, feasible and effective method of ultra performance liquid chromatography (UPLC) coupled with photo diode array (PDA) were established for fingerprint analysis and simultaneous quantification of three major classes of constitutions including iridoid glycosides, crocins and organic acids of fructus Gardeniae. Extraction method was optimized as 75% methanol ultrasonic extraction for 30 min. Acetonitrile-water (containing 0.2% formic acid) gradient elution on Waters Acquity BEH C18 column (50 x 2.1 mm, 1.7 mu m) was used to obtain good chromatographic resolution. 24 characteristic peaks were comprised in the fingerprint common pattern. Among them, seven marked components, geniposide, shanzhiside methyl ester, geinpin, geniposidic acid, crocin I, crocin II, and chlorogenic acid, were quantified. Similarity evaluation, principal component analysis and hierachical cluster analysis were applied to demonstrate the distinction. It was concluded that chemical components of Gardenia jasminoides Eills and Gardenia jasminoides var. radicans Makino from different origins were similar. Other than determination of the content of geniposide and crocin I, comparison of fingerprint atlas could be considered as a suitable quality control method for fructus Gardeniae.