Against the backdrop of intensifying market competition and industrial chain restructuring, homogenized competition has become a core bottleneck for SME development. Policies such as the “14th Five-Year Plan for Promoting SME Development” explicitly advocate supporting SMEs in pursuing a differentiated development path characterized by specialization, refinement, distinctiveness, and innovation. This paper employs the ecological niche theory as an analytical framework to systematically dissect core challenges in SME differentiation, including ambiguous niche positioning, blind differentiation direction, weak resource integration capabilities, and insufficient dynamic adaptation. It proposes three differentiation strategies: niche separation, expansion, and optimization, while constructing end-to-end implementation strategies across precise positioning, resource integration, and dynamic adjustment dimensions. This research provides theoretical support and practical pathways for SMEs to break through competitive barriers, respond to policy directives, and achieve sustainable development.