Efficient utilization of lignocellulose is crucial for carbon emission reduction and decreasing reliance on fossil fuels. Building on a previously proposed methanol-based functional group protection strategy, which simplifies lignin-carbohydrate separation and prevents lignin condensation, this study thoroughly assesses its environmental impacts using life cycle assessment principles. Compared with that of six established pathways, the novel process can reduce composite environmental impact by up to 54%. Subsequently, integrated energy-environment-economy evaluation models were innovatively developed for an in-depth analysis. Across various comprehensive assessment frameworks, integrated modeling reveals certain ranking variations but enables robust decision-making. Notably, lignin valorization can enhance significant benefits of biorefineries. Corn-stover cellulosic biorefinery, which integrates lignin gasification-syngas fermentation to produce ethanol, and poplar cellulosic biorefinery, which integrates lignin depolymerization for antioxidants co-production, perform optimally. Finally, the study proposes optimization recommendations and underscores the importance of further research to develop innovative models or tools to improve the policy support system.