Abstract:The paper uses the SE-DEA model to evaluate the efficiency of science and technology innovation of 21 cities in Guangdong in 2018, gets ranking result, including 12 cities reached DEA effective. The evaluation results are as follows: Guangzhou ranked first, Zhaoqing ranked the last, Shenzhen ranked the first in the input-output index, only ranked eighth in the evaluation value of science and technology innovation efficiency, which shows that the efficiency of scientific and technological innovation has no great correlation with regional economy, and it is not that the more personnel and funds input, the higher the efficiency, if there is no corresponding proportion of output, the efficiency value will be reduced.