Herein, we demonstrated the synthesis of pharmacologically significant 3-methyl-4-(hetero)arylmethylene isoxazole-5(4H)-one by employing the water extract of lemon fruit shell ash (WELFSA) and glycerol as a solvent medium. The present method explored WELFSA as an eco-friendly catalyst to obtain 3-methyl-4-(hetero)aryl methyleneisoxazole-5(4H)-one derivative by the reaction of substituted aryl/heterocyclic aldehyde, hydroxylamine hydrochloride and ethyl acetoacetate at 60 ◦C on oil bath stirring condition. The completion of the reaction was monitored by thin-layer chromatography, and then the reaction mixture was quenched with ice-cold water, the separated solid was filtered, recrystallized in ethanol, and confirmed by various spectroscopic techniques. Some of the selected derivatives are subjected to DNA cleavage studies against pBR322, and showed comparable activities.