The regional differentiation of Middle and Large sized Euterprise(MLE) technological innovation in China is researched form the angel of input-output. Firstly, wide gap coefficient is applied to analyze the regional differentiation of MLE on the industrial output value of new products, expenditures of technological activities, and the number of scientists and engineers in China as a whole. Then, using panel data, the structural influence of input on output about 30 provincial medium-sized and large-sized enterprises’ technological innovation is thoroughly analyzed, the structural differentiation is found out and the cause is explained. In conclusion, some pertinent measures to improve MLE technological innovation ability for each province are put forward.