Cordyceps militaris is an important medicinal and edible fungus that contains a wide range of bioactive ingredients, including cordycepin, polysaccharides, ergosterol, mannitol, proteins, and carotenoids, which collectively confer tonic, anti-fatigue, immunopotentiating, antioxidant, anti-inflammatory, and metabolic-regulating properties. Notably, the culture residue of C. militaris, which remains rich in bioactive compounds, is mostly discarded during production, resulting in resource waste and potential environmental pollution. In this study, C. militaris culture residue extract (CME) was prepared by ultrasonic extraction, and its antiviral activity was evaluated using Nicotiana benthamiana via foliar spraying. The results showed that CME treatment significantly upregulated the expression of defense-related genes PR1, PR2, and ICS1, with PR1 showing the most pronounced induction (13.20-fold before and 11.89-fold after TMV inoculation), thereby conferring strong antiviral activity. In addition, root irrigation with 10 mg/mL CME significantly increased plant height, stem diameter, dry weight, fresh weight, chlorophyll content, and carotenoid content in tomato plants. Taken together, these findings indicate that CME functions as a plant immune inducer capable of effectively suppressing tobacco viral diseases while promoting plant growth. This study not only provides a new strategy for the value-added reutilization of C. militaris culture residues but also offers a scientific basis for the green control of tobacco mosaic disease.