The article presents the results of a comprehensive system-dynamic study of the influence of institutional factors and human capital dynamics on corporate innovation processes, with a focus on the phenomenon of international scientific migration (“brain drain”). The methodological basis includes a network analysis of temporal structures of migration flows, system-dynamic modeling described by a system of nonlinear differential equations for stocks and flows of scientific human capital, econometric modeling of macroeconomic determinants of emigration and discourse analysis. Critical institutional dysfunctions are empirically identified, in particular, the low level of recognition of the scientific community as a strategic asset in Russia, which correlates with the high intensity of emigration and the growth of the underemployed scientists sector. It is established that structural imbalances in national innovation systems, mismatches between qualifications and wages, and the extensive nature of investments in human capital suppress corporate innovation potential. The key condition for its restoration is the need for strategic reinvestment, support for “strong innovations” capable of forming competencies adequate to the socio-cultural context. The results provide tools for developing scientific and technical policies aimed at retaining human capital and stimulating innovation in the corporate sector.