Aqueous extract of Nardostachys jatamansi DC. (AENJ) is well-known for activities such as alleviating acute pancreatitis, improving cardiac function, and suppressing melanin synthesis. However, quality control of the underlying chemical constituents has not yet been explicitly raised. To tackle the issue, thirty-eight batches of N. jatamansi were collected, and an ultra-high-performance liquid chromatography (UHPLC) method was established by coupling with the fingerprint of traditional Chinese medicine and similarity analysis. Then, seven common peaks were selected with batch similarity > 0.939 by the fingerprint similarity model, and a total of seventy-one joint constituents of AENJ were tentatively identified by UHPLC-Quadrupole Time-Of-Flight Mass Spectrometry (QTOF-MS) analysis and comparison of their chromatographic and mass profiles with those of standard substances and/or reported ones in literatures. Among them, desoxo-narchinol A (DA, 10 μM) and nardosinonediol (ND, 1 μM), the predominant constituents, as well as the extract AENJ (100 μg/mL), exerted their significant whitening potentials by reducing the melanin content (1.46 ± 0.19 %, 0.90 ± 0.10 %, and 1.27 ± 0.21 %, respectively) and inhibiting the tyrosinase activity (1.05 ± 0.05 %, 0.89 ± 0.28 %, and 1.29 ± 0.38 %, respectively) in B16F10 cells induced by α-MSH. Finally, both DA and ND were selected as the quality markers of AENJ, and an UHPLC-DAD method was established for simultaneous determination of their contents as 2.382-9.051 and 0.931-4.218 mg/g, respectively. Our study was dedicated to the quality control of AENJ in future applications and development of N. jatamansi extracts, components, or derived products in the world of whitening.