The paper use grey relational analysis and lag coefficient method to calculate the lag phase and lag coefficients belong to different lag phases. Inspired by combining method of Super-SBM model and window analysis, the paper introduces the improved DEA model which calculate the time lag between S&T input and output to evaluate the relative efficiency of nine advanced manufacture industries in Fujian province. DEA window analysis can measure relative efficiency of the same decision unit in different time.Super-SBM model not only fully consider the slack problems, but also differentiate the efficient DMUs, it can make the efficiency evaluation process of S&T input and output more suitable to the actual.