Abstract: The running situations of sci-tech special commissioner system in 13 counties in 4 cities include Fuzhou, Putian, Quanzhou and Sanming were investigated by using questionnaire survey and interview methods. Base the survey data, the operational performance of sci-tech special commissioner system was analyzed, and the existing problems were summarized. Finally, the countermeasures for optimizing sci-tech special commissioner system in Fujian were put forward.