This study is expected governmental R&D investments in situations where there is a problem of efficiency in government R&D investment and investment performance continued being raised is evaluated as to whether you can have an impact on corporate performance. So, This study classified 40 Industries, which are divided into the leading growth industry and the main industry, focusing on the second stage of the Leading Industry Development Project for Economic Region, to the similar industry between the representative flagship and the growth leader based on KSIC. Through this, Government R&D budget affects the management performance by industry and company size, and the business performance when it is invested in Regional companies. Based on the results of this study, we propose a policy direction for efficient investment of R&D. In order to analyze the performance of government R&D investment, the Bio·Medical industry (regional project) was selected from among the leading industry development project. For the analysis, we selected biotechnology and medical industry (local business) among the Leading Industry Development Project for Economic Region that were promoted for three years from 2012. Analysis indicators we analyzed the enterprise (large, medium-sized enterprises, SME) productivity indicators (gross value-added per capita, sales per capita) with growth indicators (net sales growth rate, operating profit growth rate, net profit growth rate, asset growth rate, employee growth rate). The productivity indexes of companies(large, small and medium enterprises) that received R&D support from government by selecting biotechnology and medical industry (regional business) among the large-area leading projects that were promoted for three years from 2012 (value added per employee, Sales growth, operating profit growth, net profit growth, total assets growth, and employee growth rate). As a result, both the representative flagship industry and the growth leading industries showed an increase in sales per capita, which is an indexes of productivity, over time. The value added per employee, which is the most important productivity index, measures profits attributable to a wide range of stakeholders. The average value of the representative flagship industries is higher than the growth leading industries. We find that government R&D investment has a positive effect on firm performance, as both the total assets growth rate, the net profit growth rate and the number of employees increase. Even in the case of similar industries, we could confirm the difference between industrial classification, company size, and financial characteristics between the growth leading industry and the representative flagship industry. In addition, a t-test was conducted to obtain statistical significance for the analysis. The limitations of this study are that the size of SMEs participating in the project varies, and it is necessary to compensate the difficulty in distinguishing the differences on the error bar. From this research, in the future, it is necessary to set direction for government R&D investment through comparative analysis of 40 industries.