Nymphaea rubra flowers (NRF) are widely used as a food and in folk medicine throughout the subtropical regions due to their health-promoting characteristics. This study characterized the phytochemical composition of various extracts/fractions of NRF by establishing a quadrupole–cyclic ion mobility–time-of-flight (Q-cIM-TOF) mass spectrometry method in both positive and negative electrospray ionization modes. Over 100 phytoconstituents were tentatively identified, among which 53 phytochemicals belonging to phenolic acids, tannins, flavonoids, terpenoids, alkaloids, xanthones, and naphthopyrones have never been documented in NRF before. Moreover, the ethyl acetate fraction of NRF demonstrated strong antioxidant potential (IC50: 9.21 ± 0.47 μg/mL in DPPH assay and 13.65 ± 0.03 μg/mL in ABTS assay) and tyrosinase, α-glucosidase, and elastase inhibition (IC50: 10.58 ± 0.20, 2.48 ± 0.02, and 38.15 ± 0.25 μg/mL, respectively). The findings highlight the value of NRF as a source of functional components and broaden its potential applications in the food and nutraceutical industries. © 2022 Elsevier Ltd