Using DEA model and DEA-Malmquist productivity index method, this paper conducts an empirical study of technological innovation efficiency and inputoutput situation, as well as total factor productivity from the changing of time and space, by collecting the panel data of input and output of technology innovation of Hunan’s 14 cities and counties from 2011 to 2015 and by using the DEAP software. The results are as follows: there was still some redundancy between capital and manpower investment in some cities and counties of Hunan Province, and these cities and counties can’t make full use of technological innovation resources; the conversion rate of technological innovation was low and the output was significantly insufficient in some cities and counties of Hunan Province; the efficiency of technological innovation was relatively low, total factor productivity growth was small, and the management level of technological innovation needed to be improved in Hunan Province. Combining the output level of each city and county, Hunan Province should rationally allocate and make full use of each input resources to avoid the waste of resources. Hunan Province should also accelerate the transformation of technological innovation results into productive forces and improve the social and economic benefits of technological innovation. According to local conditions, it should rationally optimize the level of technology innovation management, promote the dual driving effect of technology progress and technology efficiency to the technology innovations, thus improving the overall efficiency of technology innovation.