Against the backdrop of the digital economy, intellectual property has become the core competitiveness of small and medium-sized enterprises (SMEs). As an in-depth integration of emerging technologies and traditional financial management, intelligent accounting provides new solutions for SME intellectual property protection. This paper first expounds the significance of intelligent accounting for the protection, then analyzes the prominent problems faced by SMEs, such as imperfect accounting and evaluation systems, low informatization level and weak protection awareness. On this basis, it proposes specific countermeasures including building an intelligent accounting-driven intellectual property asset management system, conducting risk early warning and monitoring via big data analysis, and establishing a full-life-cycle intelligent financial management mechanism, aiming to offer theoretical and practical references for SMEs’ intellectual property protection.