Plant-based phytoconstituents have been in use against larvicidal, pupicidal, and repellent actions, which have gained increasing popularity in recent days and are safe when compared to synthetic insecticides. In this study, seven ligands were found from C. gigantea and S. kunthiana leaf ethanol extract using GCMS. The target protein, carboxylic ester hydrolase, from Cx quinquefasciatus, was taken from the UniProt database. It was predicted the 3D structure of the target protein and the sequence identity was 69.49%. The best model was chosen and evaluated using the Ramachandran plot. 88.2% of residues are located in the most favoured regions, which confirm that the predicted model is good. According to molecular docking studies, all seven compounds interacted with the target protein. Among the 7 compounds, Neophytadiene (-6.2 Kcal/mol) showed very good interaction with the carboxylic ester hydrolase (target protein). Hexadecanoic acid showed the lowest binding affinity (-5.3 Kcal/mol) with the amino acid residues of the target protein. The ADMET and CYP properties were tested for the phyto-compound Neophytadiene. The good binding affinity of phytocompound neophytadiene obeys the Lipinski rule of five, and the compound did not cross the blood—brain barrier (BBB) and has low intestinal absorption (HIA). The fractional CSP3 value is within the range of rotatable bonds of the compound. The CYP property of the compound does not inhibit most of the CYP450 enzymes and does not cause any adverse reactions, but it inhibits only the CYP2C9 enzyme. The neophytadiene value of log Kp (Skin Permeant) is -1.17, showing less skin permeant, and a bioavailability Score (ABS) of 0.55 shows that it passes the rule of five.