Agricultural production in India mostly affected due to the parasitism of different pathogens, parasites and pests among them root knot nematodes (RKN) creating major problem in agricultural production which is directly shows effect on Indian economy. Meloidogyne incognita a nematode parasite which can infect almost 2000 different plant species. Peroxiredoxin is responsible for the defense response against plants and also responsible for causing nematode infestation in plants. It has been reported that Peroxiredoxin protein serves as a vital drug target to inhibit their growth and development. Inhibition of peroxiredoxin from nematodes may helpful to plants as it plays important role in plant defense mechanism. Current study aims to find phytochemicals which can be used as natural inhibitors of M. incognita by targeting Peroxiredoxin. To understand the structural and functional aspects of peroxiredoxin it is prerequisite to explore insights of protein primary, secondary structure and tertiary structure. In present study computational prediction of primary structure of Peroxiredoxin protein of Meloidogyne incognita is performed using Uniport. The physicochemical property analysis of peroxiredoxin protein were obtained from EXPASY server ProtParam. In secondary structure analysis amino acid composition of peroxiredoxin were predicted by PredictProtein. Three-dimensional structure of Peroxiredoxin from M. incognita were predicted by using Homology modeling approach three-dimensional structure of Peroxiredoxin was determined using protein structure prediction server (PS2 Server) selecting MODELLER as structure prediction method, predicted structure of protein also gets validated by using various validation tools. The AutoDock automated docking software were used for molecular docking and predicting optimal protein ligand interaction. Based on ADMET properties analysis and binding affinity all the three phytochemicals Withaferin A, Triptolide and Indole 3 Acetic acid shows nematocidal properties.