Abstract: To comprehensively measure the construction achievement of 12.5 m deepwater channel project of the Yangtze River downstream of Nanjing, based on the fundamental principles of value orientation and internal logic and the relationship chain of “Values-Goals-Objectives-Criteria and Standards”, we used the positive and negative deductive analysis to propose a set of performance evaluation indexes for the major state construction project that strictly follows the project objectives and closely links with the project content. According to the expert questionnaire survey, the performance evaluation index set was confirmed. The results indicate that compared with the existing performance evaluation index guidance for inland waterway engineering, the proposed index set not only focuses on the project’s construction achievements, but also pays more attention to the implementation of the strategic value for the regional and national development by revealing the relationship between the project and the national economy, social development, resources and environment comprehensively.