Masson pine wood is widely used in living spaces, decoration, and construction. Owing to its high sugar content and tendency to mold. Masson pine wood has been treated with anti-mildew agents. As environmental awareness grows, replacing traditional anti-mildew agents with environmentally friendly agents is crucial. In this study, a lignin-derived microcapsule anti-mildew system was created by solvent exchange and self-assembly using hexadecyltrimethylammonium bromide (CTAB)-modified enzymatic hydrolysis lignin (EHL) as the shell and cinnamon essential oil (CEO) as the core. After vacuum high-pressure impregnation with the CTAB-EHL@CEO microcapsules, the wood exhibited outstanding anti-mildew performance against Penicillium citrinum, Trichoderma viridis, and Aspergillus niger. With 0.6 mg/mL CTAB-EHL@CEO, the mildew grade of the wood reached zero. Moreover, the microcapsules were stabilized by hydrogen bonds formed between the amino groups of CTAB and the hydroxyl groups inside the wood, boosting the anti-loss performance. Using 0.3 mg/mL CTAB-EHL@CEO, the encapsulation of EHL-CTAB significantly increased the CEO load in the wood from 21.521 to 48.729 μg/cm