Firstly, this paper determines the variables and form of the stochastic frontier function. Then it studies the R&D Input-Output efficiency ，influencing factors and convergence by the approach and the panel data model. The empirical result shows as follows: R&D capital input, R&D labor input and new product research and development investment have significant effects on new product output value and the effect of R&D labor input is larger; the R & D input-output efficiency of advanced manufacturing in Fujian province centers on the whole and takes on a increasing trend and the convergence; the number of firms and government funding of its R & D has a significant effect on the R & D input and output efficiency within nine industries during the sample period. Finally, the study found the countermeasures and solutions, which the corporate and government should take in the development of R&D.