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Regional innovation system is a vital component of the national innovation system, as well as the base of the development of the regional economy. At present, the shortage of human resources and financial resources is the main obstruction for the improvement of the innovative capacity of the regional innovation system. Meanwhile, the structure of both inputs and outputs of regional innovation system gradually becomes a vital factor influencing the improvement of resources allocation efficiency. Due to certain constrains of macroeconomic factors, the shortage of the human resources and financial resources can not be met in a short period. Consequently, strategy of resources allocation improvement, analyzed by the view of the structure of the inputs and the outputs of regional innovation system, is a very heated topic, influencing both the innovative efforts of the firms and the sustainable development of the regional economy. The paper analyzes the structure of the inputs and outputs by the method of exploratory factor analysis firstly, and then evaluates the resources allocation efficiency of regional innovation system from 1995 to 2004 by utilizing the data envelopment analysis benchmarking method. Based on the empirical results, the paper proposes three strategies to improve resources allocation efficiency of regional innovation system: firstly, the structure of the inputs and outputs should be given more attentions. The increase of resources inputs alone cannot get expected outputs, but decrease resources allocation efficiency of RIS if adjustment of the inputs' structure is ignored; secondly, the amount of the financial inputs should be determined according to the stock of the human resources; Thirdly, the policy-maker should consider which stage regional innovation system is in. Precisely, the enhancement of commercialization of S&T, the increase of S&T outputs and the improvement of quality of the S&T outputs should be, in order, the main focus- to improve resources allocation efficiency, according to the stage of thedevelopment of the regional innovation system.