Abstract Basic research is the source of scientific and technological innovation. It is particularly important to strengthen basic research for Guangdong and Jiangsu, which are strong economic province and big science and technology province, and are implementing independent innovation strategy and innovation driven development strategy. Based on constructing the evaluation index system of basic research, taking Jiangsu as a reference object, the fundamental research development status quo of Jiangsu and Guangdong provinces were analyzed, and a further study on the basic research ability of two provinces was made by Analytic Hierarch Process. It is concluded that the investment in basic research in Guangdong has been increasing year by year and has achieved good scientific and technological achievements. Enterprises have certain advantages in basic research. With the analysis of the relevant data and indexes from 2000 to 2014 by Analytic Hierarch Process, the level of Guangdong's basic research ability at the provincial level is 82.5 points，but the one at the institution-university level is only 46.5 points in 2014. Compared to Jiangsu（the provincial level is 92.4 points，the institution-university level is 94.2）,Guangdong's basic research ability is weak, output is less, the development space of basic research ability of research institutions and universities is larger. While promoting Guangdong universities and research institutions to increase input and output of basic research, and vigorously enhance their basic research capabilities, actively promote "government- industry-university-institute" cooperation in the field of basic research, play a good role of enterprises.