Building a maritime power is a strategic task for the great rejuvenation of the Chinese nation. As a traditional maritime power, Russia plays an important role in global marine scientific and technological innovation. A thorough understanding of Russian marine scientific and technological innovation management system can provide useful lessons for China’s marine scientific and technological innovation in the new development stage. This paper analyzes the Russian marine science and technology innovation management system from three aspects: the structure of the Russia’s marine science and technology management system, marine science and technology innovation agency, and marine science and technology innovation strategy. It summarizes the characteristics of Russia’s marine science and technology innovation management system: A sound innovation system lays the foundation for marine scientific and technological innovation management; High-level marine strategic planning guides the priority direction of marine scientific and technological innovation; The lack of diversity of scientific research funds poses a challenge to its marine science and technology innovation activities; The particularity of land and sea locations leads to the specificity of innovation system. Combining with the current situation of China’s marine science and technology, relevant suggestions are proposed: Enhance the innovation ability of marine science and technology management system and mechanism; Continuously optimize the system of marine scientific and technological innovation force system; Strengthen strategic research on marine science and technology; Actively seek bilateral cooperation between China and Russia in the maritime and polar fields.