By retrieving the clinical research literature of treatment functional dyspepsia by traditional Chinese medicine (TCM) from January 2004 to December 2014 based on China National Knowledge Internet (CNKI), we would establish a TCM decoction database for treating functional dyspepsia in this study. One hundred and sixty-four literature were included, involving 159 prescriptions, 377 medicines, in a total of 1 990 herbs. These herbs can be divided into 18 categories according to the effectiveness; and qi-regulating herbs, blood circulation herbs, and antipyretic herbs ranked top three ones according to the frequency of usage of the herbs, whose medicine usage frequency accounted for 51.81%. Usage frequency of 16 herbs was over 30, and Atractylodes, Radix, Poriaranked top three according to the usage frequency. Medicinal properties were divided into 9 kinds according to the frequency statistics, and the top three were warm, flat, and cold. Taste frequency statistics were classifiedinto 9 kinds, and the top three were acrid, sweet, and bitter. In frequency statistics of the meridian tropism of herbs, it was classifiedinto 11 kinds, and the top three were spleen, stomach, lung. The analysis can provide a reference for treatment and study of TCM of functional dyspepsia.