In today’s knowledge economy era, the transformation of scientific and technological achievements is an important driving force for promoting economic growth and social progress and intellectual property protection is an indispensable safeguard mechanism in this process. This paper focuses on the collaborative mechanism between intellectual property protection and the transformation of scientific and technological achievements, and explores its role in promoting scientific and technological innovation, economic development, and social progress. The study shows that intellectual property protection provides a solid legal and institutional foundation for the transformation of scientific and achievements by clarifying the property rights of scientific and technological achievements, incentivizing the enthusiasm of innovative entities, and enhancing the market value of technological achievements. However, the current collaborative mechanism still faces numerous challenges. This paper proposes a series of optimization strategies, providing a theoretical foundation and practical pathways for the implementation of an efficient collaborative mechanism for intellectual property protection and transformation of scientific and technological achievements. These strategies hold practical value for propelling technological breakthroughs and socio-economic advancement.