With China’s development from the “world’s factory” in the past to today’s increasingly prominent role as the “world’s R & D laboratory”, to the world’s important innovation plateau in the future, the status and role of its higher education have been changing, and the importance and order of the scale, structure and quality of higher education in the development of innovation have also changed. Based on the decomposition framework of the effects of higher education scale, structure and quality on innovation and provincial panel data, the empirical analysis using mixed regression, Shapley value decomposition, double fixed-effects model and systematic generalized moments estimation found that: (1) the scale, structure and quality of higher education significantly affect regional innovation, and with the upgrading of the stage of innovation development, the status and role of higher education have been increasing, in which the importance of structural optimization and quality improvement is increasing, while the importance of scale expansion is relatively declining; (2) the contribution of higher education scale expansion to regional innovation increment (patent output) is about 14%, accounting for about half of the total contribution of higher education, reflecting the fundamental status of the scale effect; (3) the quality has a more consistent and significant positive effect, for every 1% increase in the quality level of the per capita student population, the patent output grows by an average of 0.7%~1.1%; (4) the hierarchy has a non-linear effect, and there is a synergistic interaction effect with the scale. The growth of total innovation can be driven by the scale of postgraduate education, and the growth of invention and innovation needs to rely on the synergistic effect of the expansion of the total scale and the increase in the proportion of postgraduate students. For this reason, China’s higher education development mode relying on the incremental scale needs to be shifted to the “stock optimization” mode mainly focusing on structural optimization and quality enhancement, and implement the regional differentiated development strategy of “classified positioning, layered expansion, and comprehensive quality enhancement”. In addition, the leading original innovation zones need to strengthen the synergistic layout of high-level education, and technology diffusion carrying zones should consolidate the foundation of undergraduate education. Also, localities should build a layout system that fits the stage of innovation with the core of quality leap.