In modern conditions of the innovative development, human capital investments are made under the project economy which is based on the project as an organizational unit of coordination and a principle of partnership as a way of coordinating the investment activity of participants. The paper proposes an approach to determining the institutional framework for the projects and the relevant contractual relations between participants of the investment activity within financing investments in the human capital at the microeconomic level.The paper shows that training costs may be taken into account to evaluate investment projects in different ways, which leads to various economic and financial consequences. This estimation of investment projects is not limited to a tight framework of commercial (financial) efficiency and includes the analysis of public (economic) efficiency as an important component. The application of such an approach is necessary for innovative projects with a significant gap between financial and economic efficiency, and which demand implementation on principles of the public- private partnership. The methodology of the commercial (financial) efficiency evaluation is proposed for different types of the institutional design of the interaction between participants, who invest in education and training. The simulation model of the investment project was developed as a tool for evaluating the efficiency with a detailed representation of direct and indirect public funding to cover training costs. In order to determine financial effects of the state support, the author used indicators of net present value, calculated on the basis of relevant changes in cash flows. The proposed methods and models are implemented in practical calculations of training costs in the project of nanoceramics production using multivariate experimental studies of contractual relations between the project participants.