Abstract: It establishes two-stage series DEA model, researches science and technology input and output efficiency, the first-stage science and technology innovation and second-stage science and technology application.By selecting the 8 years data from 2006-2013, it evaluates and analyzes the city science and technology input and output in Henan province.The result shows: (1)some cities’science and technology resource allocation mechanism are weak; (2)Zhengzhou city technology efficiency is better than other cities.