The study highlights the importance of interaction between innovation, competitiveness and foreign trade. This study found the innovation competitiveness of a country is the main determinant for successful integration of country in the Global Value Chains (GVC). The purpose of research is to study the most problematic factors that affecting the innovation competitiveness of the Moldovan economy. The study is based on the analysis of the Republic of Moldova’s score and position in international indicators and rankings in correlation with the methodology of the World Economic Forum. The values of innovation, business sophistication and technological readiness factors of competitiveness between Moldova and South- Eastern Europe countries are analyzed in the paper. The study identified that the Republic of Moldova and Serbia recorded low indicators of the innovation and sophistication competitiveness in comparison with other countries of Southeast Europe. At the same time economy of Moldova follows the EU economies on the technological readiness, overcoming the Albanian and Serbian economy in the last years. The study showed that the need to raise the competitiveness by attracting foreign direct investments into research and development, information communication technologies as well as the high-value manufacturing and tradable sectors and by fully and efficiently implementing public institution reform, has become not only important but also urgent because the country is to be capable to strengthen the economic benefits that many countries have reached in past years. The results of study can be used in process of implementation of public administration reform, the elaboration of the National Program of science and innovation of the Republic of Moldova, the improving of governance the research and development in country.