The purpose of the research is to look for the new ways of the investigation of the subsidy impacts on research and development (R&D) investment and company’s innovation performance. Methodology of research based on the papers type or theoretical approach. Innovation performance measured by firms’ success in bringing innovations to the market, the share of sales that can attributed to products that were new to the market. R&D efficiency is the essential factor for company’s innovation performance, it is the link between R&D input and output. The Triple Helix (TH) model assumes that the driving force of economic development in the post-industrial stage is the production and dissemination of socially organized knowledge. Institutions that generate knowledge increasingly play a role in the networks of relations among the key actors: University (Science), Industry (Business), and Government (Governance). Nowadays the impact of the external environment in particular is critical for innovation under different kinds of the uncertainty. Targeted innovation policy design fosters innovation performance, that is, whether the publicly induced part of the R&D investment translates subsequently into product market innovations. New research framework is created for practical implementation.