Herbal medicine constructs the base of today’s therapy as the plants provide an infinite source of nutraceuticals. Employing herbal medicines in managing the microbial infections is a trend of today’s world. The search for new antiinfectives, especially antimicrobial drugs, is still in demand. In most of the researches, bark, root and leaves of plants are used as drug in the treatment of various therapies but flowers are not much studied. In this study, Senna alata flowers are selected for novel phytoconstituents and its anti bacterial activity that is supported by molecular modeling against Staphylococcus pneumoniae. When compared to other extracts studied, aqueous extract of C.alata flowers showed a high content of secondary metabolites and flavonoids, alkaloids, terpenoids. Aqueous extract of C.alata flowers by GC-MS analysis showed the detailed peak of 30 compounds, nearly 14 hit compounds are detected and the top two higher composition of compounds identified are camphene (RT=4.727) tocopherol, (RT=5.695) iosorbide dinitrate. In the antibacterial study of C.alata flowers, the zone of inhibition is close to the standard tetracycline and to scrutinize the possible mechanisms behind the antimicrobial activity of phytochemicals in C.alata flowers, molecular docking is carried out. Flowers of C.alata consist of high content of Camphene, a terpenoid that can easily diffuse across cell membranes to reduce the opportunity for bacteria to develop its resistance. The top compound called camphene is docked against the MurF1 protein of Staphylococcus pneumoniae that showed the binding affinity is strong with binding energies -8.8 Kcal/mol. Phenolic compound called isosorbide is predicted to exert strong inhibition against MurF1 protein Staphylococcus pneumonia