This paper applied nonparametric DEA trans-efficiency method to the evaluation of the efficiency of science and technology of nine cities of Fujian Province from 2004 to 2007, again applied Malmquist index to analyze forming reasons and dynamic productivity variation of non-DEA efficiency regions of the efficiency of science and technology of Fujian Province. Positive results show that the efficiency of science and technology of cities of Fujian Province generally shows a upward tendency, yet there exist a relatively great disparities in scope and efficiency of the science and technology input and output between different regions. And the increase of productivity is mainly contributed by the improvement of technology, while the efficiency of technology needs improvement.