Salvia moorcroftiana is a medicinal plant found in the Himalayan mountainous range, common in the Kashmir Valley, traditionally used to cure various ailments. In this study GCMS, GCGCTOFMS and LCMS/QTOF/Orbitrap spectroscopic techniques were used for comprehensive phytochemical profiling of seed oil obtained through hexane extraction. Additionally, in vitro antioxidant, anticancer activities, Thermogravimetry cum Differential thermal analysis (TGADTA) and amino acid profiling were evaluated. The seed oil revealed linoleic acid as major phytochemical through GCMS (84.94%) and GCGCTOFMS (29.36%). High Resolution Liquid Chromatograph Mass Spectrometer detected presence of phenolic, flavonoid, monoterpenoid, sphingolipids, coumarins, fatty acid derivatives compounds. Seed oil was found to be moderate for radical scavenging potential with IC 50 values of 206.79µg/ml,199.04 µg/ml and 171.72µg/ml in DPPH, ABTS and FRAP scavenging assays and total antioxidant capacity was 92+4.79 (mg AAE/g dw). The phenolic (TPC=32.11±2.43 mg GAE/g dw) and flavonoid (TFC=15.34±3.71 mg RE/g dw) contents of the seed oil were also assessed. The seed oil demonstrated strong in vitro anticancer activity against HCT-116 (GI 50=26.38 µg/ml), HeLa (GI 50=28.89 µg/ml), MCF-7(GI 50=31.60 µg/ml) and A-549 (GI 50=46.82 µg/ml) cancer cell lines, was carried by MTT assay. The seed oil comparatively showed less cytotoxicity with GI 50 value of 140.12 µg/ml towards normal cell line (L-929). DAPI and Rhodamine 123 dyes confirmed disruption and alteration of nucleus and mitochondria in cancer cell lines. TGADTA evaluation supports optimum thermal stability and degradation patterns of seed oil. Essential amino acids like isoleucine, phenylalanine, threonine, and tryptophan among others were present in seeds. This study presents a potential future strategy to drive the pharmaceutical, nutraceutical benefits from seeds of Salvia moorcroftiana.