Objective To construct the network of Chinese medical formulas and Chinese medicinal chemical space

and analyze their properties and explain TCM theory of prohibited combination.Methods The network of Chinese medical formulas was built up by using complex network technology and software such as Pajek and ORA.The properties of this network were analyzed including network diameter

average distance

clustering coefficient and average degree.The Chinese medicinal chemical space was constructed through describing descriptors calculation

focus treatment and space dimension reduction on the base of chemical space theory

and the properties like space distance of this space was calculated and analyzed.The properties of doubled herbs in eighteen herbs of mutual antagonism and nineteen incompatible herbs was studied based on above network of Chinese medical formulas and Chinese medicinal chemical space.Results The network of TCM formulas was a partial scale-free complex network combining the property of small-world network.The chemical discrete property of Chinese medicinal chemical space and bulk property of Chinese medicinal were consistent.The results of data analysis were accorded with the properties of doubled herbs in eighteen herbs of mutual antagonism and nineteen incompatible herbs through network path analysis and distance measurement of chemical space.Conclusion TCM theory of prohibited combination is supported by the theory of network of TCM formulas and chemical space and has a scientific foundation.The study has given a new insight into the research of TCM theory of prohibited combination.