To study the morphological and anatomical characteristics of Coptis deltoidea based on the research of its breeding system.The flowering process of C. deltoidea was observed dynamically and the out-crossing index was estimated, using Motic BA200 microscope to observe the morphologic characteristics of the mixed bud, stolon and pollen was observed microscopically, and compared with those of C. chinensis.The results showed that the breeding system of C. deltoidea was facultative hybridization, it could bloom normally and fruit while cannot form seeds. And there were no statistical differences in the number of stamens, pistils, ovules, pollens in a stamen, pollens in a flower, pollen-ovule ratio, and the pollen grain size between C. deltoidea and C. chinensis. However the pollen of C. deltoidea developed anomaly, most of the pollen grains in it were surface depression, the texture was unsharp or broken, the pollen could not germinate. The lateral bud on the lower side of the mixed bud formed in the bud stage. Pericyclic fibers in the stolon (the vegetative propagation branch) shaped like a cap, and all the shaped-caps nearly formed a ring.The abnormal development of the pollen could be the mainly cause to the no formation of seeds in C. deltoidea. The lateral bud forming in the bud stage then developing the stolon is the characteristics of the asexual propagation. Pericycle fibers in the stolon nearly forming a ring is a secondary character to accommodate the vegetative propagation of C. deltoidea.