As a transitional zone between land and water, wetland plays an important role in ecological services. Wetland plants are the basis of ecological function. The composition and distribution of plant species are closely related to different water habitats. The Yellow River basin is an important ecological barrier for the country, and the wetland area is vast. The Yellow River wetland in Henan is an important part of the Yellow River wetland. However, the effects of waterlogged habitats on plant diversity are still unclear. In order to study the plant diversity of the Yellow River wetland in Henan Province and the influence of waterlogging habitats on its plant diversity, we utilized the method of combining quadrat and transect to investigate wetland plants in seven Yellow River wetland nature reserves in Henan Province. In these reserves, a total of 981 quadrats were set for investigation. This research focused on analyzing the composition of main flora and species of wetland plants in different waterlogging habitats. Therefore, we studied the characteristics of species diversity and community diversity (α diversity) in different habitats, and compared the similarity of plant species composition and degree of similarity between communities (β diversity) in different waterlogging habitats. Moreover, the sequence and indicator species of plant species in the seven habitats were also clearly identified. The results show that:(1) Herbaceous flora is the main flora in Henan Yellow River wetland. A total of 188 species of wetland plants, belonging to 138 genera and 56 families, were found. (2) Under different standing water conditions, the plant species richness was in the order of seasonal ponding > permanent ponding > intermittent ponding > seasonal waterlogging. In addtion, the total number of major communities was consistent with the trend of species richness. (3) There are significant differences in plant species composition among different waterlogging habitats. The similarity of plant species composition and communities between seasonal ponding and permanent ponding habitats was the highest. There were obvious dominant species and indicator species in each waterlogging habitat. The hydrological habitats of the Yellow River wetland in Henan province were significantly different in different flow segments. There are obvious differences of plant diversity and main plant groups in different waterlogging habitats in the Yellow River wetland in Henan province. Under the circumstances, we suggest giving priority to the protection of seasonal ponding habitats and reducing the occurrence of seasonal waterlogging habitats during wetland ecological construction, so that we can achieve the purpose of maintaining species diversity and giving full play to the maximum ecological value of wetlands.