Till now, the state-owned Enterprises (SOEs) still plays a vital role in Chinese economy. By using DEA model, this paper investigated the total factor productivity of listed manufacturing SOEs between 2011 and 2014. Authors’ work revealed the fact that the overall stall of total factor productivity of SOEs can be explained by the declination of technological innovations. Total factor productivity of SOEs in East China is higher than those of the rest and the productivity of SOEs in Central China has the fastest growth. Furthermore, total factor productivity of high-tech SOEs maintains a slight improvement while the data in other industries decrease by various margins. At the end of this paper, it is suggested to prioritize R&D investment, industry upgrading, and layout and appraisal system optimization in the reform of SOEs to improve productivity.