In view of the scientific protection and management of intangible assets of scientific research institutions, the importance of protection and management is expounded, and the significance of intangible assets to scientific research institutions is understood. In view of the problems existing in the management of intangible assets, the paper puts forward suggestions on three aspects: paying attention to the management of intangible assets property rights, optimizing the management mechanism of intangible assets and improving the specialty of intangible assets management. The purpose is to change the ideology of all managers, realize the value of intangible assets, and improve the protection and management system of intangible assets.