In recent years, R&D efficiency has aroused wide concern among researchers, but few studies have involved the R&D efficiency of industry clusters. This paper selects internal R&D expenditure and number of R&D personnel as an input, and number of invention patents authorization is chosen as an output. Then this paper proposes the three-stage benevolent DEA model considering cooperation between decision-making units and calculates the R&D efficiencies of 10 industrial clusters during 2008-2012. The results verify the feasibility of the model and show that: (1) R&D efficiencies have increased obviously after the environmental factors and random factors are eliminated; (2) urban per capita GDP and number of graduates have a significant positive impact on the input redundancy of internal R&D expenditure and number of R&D personnel. The proportion of government R&D funds in urban total R&D expenditure has a positive influence in the input redundancy of internal expenditure of R&D while it has a negative influence in the number of R&D personnel.