This article analyzes the particularities in governance of the Russian higher education system in the light of an innovative development path selected. Authors consider internal and external challenges of the Russian higher education, as well as analyze management practices and regulations of the state level. The study applies systemic and institutional methods and approaches. Structural and functional analyzes revealed trends revealing the multi-layered problems of management of innovation development of vocational education in Russia. The authors reject the idea of universal models and solutions, offering a conceptual approach to the design and implementation of multi-level variable system of vocational education management instead.Further on, the article suggests the innovative elements of the management model of the higher education system.