Ayurveda is largely based upon usage of herbs either singly or in combination (polyherbal). Polyherbal formulation has been used all around the world due to its curative and beneficial application. In present research work, an attempt was made to compare the phytoconstituents in Nayopayam Kwatha (An Indian polyherbal formulation) and its component Herbs. The component herbs in the polyherbal formulation were collected, authenticated and processed. Ayurvedic fomulation was prepared as per standard methodology. The prescribed ratio of Nayopayam kwatha is 10:2:2, Sida: Cumin: Ginger. Accordingly 90 g of S. cordifolia roots, 18 g of C. cyminum fruits and 18 g of Z. officinale rhizome were weighed and taken for kwatha preparation. The individual plant extracts of the three raw drugs of Nayopayam kwatha viz. Sida, Cumin and Ginger were prepared in the same standard methodology followed for the preparation of Nayopayam kwatha. The differential separation of prepared of kwatha and individual extracts was done using different solvents such as hexane, chloroform, methanol and distilled water. Preliminary phytochemical analysis, Total phenolic content assay, The antioxidant activity analysis and High Performance Thin Layer Chromatography (HPTLC) Studies were done to compare phytoconstituents in Nayopayam Kwatha (An Indian polyherbal formulation) and its component Herbs. The results of preliminary phytochemical evaluations indicate that, the highest number of different phytoconstituents was observed in the Nayopayam kwatha compared to component herbs. The comparative HPTLC fingerprinting of hexane, chloroform, methanol and water fractions of Nayopayam kwatha and individual decoctions provided valuable information on the quality of the samples and showed great variation in the number of bands and their intensities. The present study was an attempt to find out the chemical changes during the processing of polyherbal formulations by comparing it with the individual source plants. The present study also shows that HPTLC fingerprinting is a reliable method to assess these chemical changes during Ayurvedic processing. Quantitative and qualitative differences were also observed with the individual source plants and the polyherbal formulations.