For self-similar system, the final system output linked to system self-products. Selecting the R&D input-structure as the input variables, citation and GDP as the output variables, the paper attempts to evaluate the effectiveness of innovation .First, using the power-law function to test whether the regional system is a system with self-similar attribute. Second, based on RMI coefficient built by the Canadian scholar KATZ, the paper constructs the mathematical model of efficiency. The model not only can be applied to compare the output elasticity of different objects, also can be of the same object .This paper takes Liaoning province and Zhejiang Province as an example, analyses and certifies their innovative effectiveness.