The Formosan subterranean termite, Coptotermes formosanus, is a globally distributed species that feeds on lignocellulose and causes substantial economic losses annually. Current control strategy heavily relies on chemical pesticides, raising concerns about environmental impacts associated with their overuse. Allyl isothiocyanate (AITC), a plant-derived pesticide, has demonstrated significant insecticidal activity. However, its effects on key physiological and biochemical systems in C. formosanus remain poorly understood. In particular, its impact on antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), detoxification enzymes such as carboxylesterase (CarE), glutathione S-transferase (GST), and neural enzymes (e.g., acetylcholinesterase, AChE) has not been systematically investigated. Transcriptome data were used to predict coding sequences (CDSs) of antioxidant, detoxification, and neural enzymes, followed by phylogenetic analysis. C. formosanus was treated with AITC at LC₅₀ for 24 h, and enzyme activities and gene expression levels were assessed. Molecular docking was performed to evaluate interactions between AITC and the five enzymes. AITC exposure significantly increased the activities of all six enzymes. Gene expression analysis revealed differential regulation across enzyme families, with notable upregulation of AChE and several CarE, SOD, POD, and GST genes. Docking analysis indicated favorable binding affinity to target enzymes (binding energy < -1.2 kcal/mol). These findings suggest that AITC induces coordinated enzymatic and transcriptional responses in C. formosanus, providing insight into its mode of action and supporting its potential as a botanical termiticide with low environmental impact.