Based on the analysis of the performance evaluation needs of scientific research projects of tobacco commercial system in Hubei Province combined with the 3E principle, a scientific research project performance evaluation index system covering three dimensions of scientific research achievements, transformation effect and project efficiency and 12 specific indicators is constructed. According to the differences of scientific research projects in research paradigm and transformation path, it is divided into agricultural and non-agricultural categories, and different index weights are determined by analytic hierarchy process entropy weight method for classified evaluation, so as to improve the scientificity of performance evaluation. Finally, the countermeasures and suggestions for performance evaluation are putforward ，and provide inspiration and reference for the performance evaluation of scientific research projects of tobacco commercial system.