Interest in the antioxidant and antidiabetic activity of natural products are growing vastly in the modern world. Thin layer chromatography-bioautography-mass spectroscopy (TLC-bioautography-MS) plays an important role in chemico-biological screening of natural sources. TLC combined with 2, 2-Diphenyl-1-picrylhydrazyl (DPPH) free radical, α-amylase and α-glucosidase bioassay were used to evaluate antioxidant and antidiabetic activities, respectively, in different extracts of Citrullus colocynthis (Hanzal), a well-known traditional Indian Unani medicinal plant. To develop a TLC-bioautographic-MS method for DPPH, α-amylase, and glucosidase inhibitors in different extract of C. colocynthis fruits. Fruits of C. colocynthis were successively extracted with toluene, dichloromethane, ethyl acetate, methanol, and water. TLC solvents were developed, and bioautographic-MS analysis was carried out to identify the antioxidant and antidiabetic compounds. HPTLC fingerprinting analysis showed maximum numbers of band separated in dichloromethane and ethyl acetate extracts of C. colocynthis, fourteen and thirteen at 254 and 366 nm, respectively. Whereas six and five separated bands were observed in toluene extract at 254 and 366 nm, respectively showed minimum numbers of metabolites. Based on TLC-bioautography-MS, maximum number of antioxidant compounds were identified in dichloromethane extract. Except aqueous extract of C. colocynthis, all the extracts have shown antidiabetic activity. On the other hand, there were no antioxidant compounds in methanolic extract of C. colocynthis. The results of this study reveal that TLC-bioautography-MS-guided strategy used to identify antioxidant and antidiabetic compounds of C. colocynthis is very useful technique for high-throughput screening of bioactive compounds. TLC-MS bioautography is a simple and fast to enables bioactive compounds present in extracts.