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With the rapid expansion of university research budget both in amount and scale, the input-output efficiency has become a focus of research interest. Based on the analysis of the latest researches concerned, this paper is intended to investigate the advantages of applying BSC to constructing an input-output efficiency evaluation system for scientific research in universities. In addition, this paper aims to construct a strategy map and an index system by means of BSC. The findings of this paper will provide a model for the scientific research input-output efficiency evaluation for Chinese universities. [ABSTRACT FROM AUTHOR]