In order to test the comprehensive performance in the field of science-technology and education in five Marine economic zones in China, set up the construction of the performance evaluation index system based on input-process-output framework, used the two-stage DEA model, empirically evaluated the performance in 2014 of the two stages, science and technology production and industrial transformation, in the field of science-technology and education in Chinese five Marine economic zone. Results showed that in the two stages the performance level of the Shandong peninsula blue economic zone and Tianjin Marine economy scientific development demonstration area is higher, but Zhejiang Marine economy demonstration area’s performance level is lower, Fujian straits economic area and Guangdong blue ocean economic comprehensive experimental zone’s is between the two level of the performance.