More than 85% of saffron (Crocus sativus L.) is producing in 22 region of Iran [1]. The quality control and its geographical effects is the main concern behind it. In this study, we developed a chromatographic fingerprint of 22 type saffron from 22 regions of Iran. Multivariate clustering methods of PCA and HCA are used for finding similarities and dissimilarities in three wavelengths 440, 308, 254 lead to the samples divided in different class base on their HPLC fingerprints. Then as a reliable, sensitive and fast method of analysis, MALDI-TOF-MS introduced for simultaneous determination of crocins, safranal and picrocrocin. Eventually and according to International Committee of Harmonization (ICH) regulation for the validation of analytical methods parameters including linearity range for crocins, picrocrocin and safranal was obtained at the range of 22-200, 32-200 and 22-100 ng/spot respectively. Also limit of quantification (LOQ) for crocins, picrocrocin and safranal were 7.18, 10.71 and 6.76 ng/spot respectively. Finally, this work is introducing MADLI-TOF as a very fast and reliable method for quantitative metabolites profiling of medicinal plant.