Hypericum species are one of the most commonly used medicinal plants all over the world and traditional uses of the Hypericum species are mainly characterized by external applications for the treatment of dermatological disorders. The purpose of this study was to investigate the chemical compounds with anti-aging and anti-tyrosinase activities of Hypericum perforatum L., H. calycinum L., and H. confertum Choisy from Turkey and to bring innovation for further studies on developing formulations with Hypericum species for topical applications. In this study, chemical compositions of methanol extracts prepared from flowering aerial parts of the following species collected from Uludağ, H. calycinum, H. confertum, and H. perforatum were investigated by LC–MS/MS. Nine metabolites, p-coumaric acid, gallic acid, quinic acid, chlorogenic acid, malic acid, protocatechuic acid, rutin, quercitrin, and isoquercitrin were identified in all analyzed species. To investigate the anti-aging and skin-whitening properties, enzyme inhibition activity of the three species were tested against, collagenase, elastase, hyaluronidase, and tyrosinase enzymes. H. calycinum appeared the most active in all enzyme inhibition activity assays which is mainly due to its rich phenolic content. The methanol extract of H. calycinum showed the highest collagenase, elastase and hyaluronidase inhibitory activities with IC50 values of 51.24 ± 1.33 μg/mL, 55.77 ± 1.32 μg/mL and 22.17 ± 0.02 μg/mL, respectively. Additionally, H. calycinum emerged as the most potential tyrosinase inhibitor among these species with 54.30 ± 0.49% at 200 μg/mL concentration. The most abundant compounds determined in H. calycinum methanol extract are, chlorogenic acid (2595.15 ± 0.179 μg/g), quercitrin (1805.9 ± 0.98 μg/g), quinic acid (885.50 ± 0.073 μg/g) and isoquercitrin (346.16 ± 0.046 μg/g), respectively. Our study demonstrates that all three extracts, especially H. calycinum extract are potential agents to use in cosmeceuticals for anti-aging and skin-whitening purposes.