In constructing a high maneuverability and reference value to scientific research institutes in the domestic of technology innovation ability of comprehensive evaluation index system, an evaluation mode on the public kind of scientific research institutions’ scientific and technological innovation ability is established by using the evaluation theory of Grey Correlation Grade in this paper,and a comprehensive evaluation of the scientific and technological innovation ability is conducted by taking the twenty-two public kind of scientific research institutions in Chongqing as research samples．According to the evaluation results,the current situation of the public kind of scientific research institutions’ scientific and technological innovation ability in Chongqing is deeply analyzed,and then some countermeasures on improving the public kind of scientific research institutions’ scientific and technological innovation ability in Chongqing are proposed.