This paper designs evaluation index systems of technological innovation capability of medical and pharmaceutical manufacturing industry and uses data mining system with DBSCAN algorithm to evaluate them,particularly analyzes technological innovation ability of medical and pharmaceutical manufacturing industry in Guangdong. The results of comparing nationally are listed as follows. As for technological innovation capability of medical and pharmaceutical manufacturing industry,Guangdong ranks fourth; with devotion capability,Guangdong ranks fourth; with output capability,Guangdong ranks fifth; with supporting surroundings,Guangdong ranks first in 2011.