Abstract: Patent evaluations are important for assessing the output of research projects. In this paper, the authors evaluated the patent achievements during the implementation of the key project of the National Key R&D Program of China in the 13th Five-Year Plan entitled “Research and development of comprehensive control and remediation technology for agricultural non-point source and heavy metal polluted farmland”. The authors employed big data on patent information, optimized the current patent evaluation indicator system, and highlighted the assessment of technique hotspots and patent operations based on the former evaluation system, which consisted of three dimensions: technique, law, and market. The results showed that the overall evaluation of patent achievements generated by the National Key R&D Program of the 13th Five-Year Plan was acceptable, with an average rating of 71.01. Patent techniques match with market hotspots to a high degree. However, a large portion of patent achievements are insufficient for industrialization, and the quality of patent application texts needs to be improved. This study is expected to properly evaluate patent outputs from research projects, recognize patents with high value, and provide methodology and case study examples for the scientific management of research projects. Meanwhile, it provides relevance for scientific research institutions to strengthen patent output, management, and applications, and to promote the transformation and application of technological advances.