Multiple natural and human factors in estuarine wetlands result in complicated land surface characteristics with distinct spatial and temporal heterogeneities, thereby contributing to the difficulty in identifying spatiotemporal variations and influencing factors of plant diversity. A unique estuarine wetland gradient system (UEWGS) consisting of soil, vegetation, heat, distance, landscape, and anthropogenic gradients was established based on the ecological features of estuarine wetland through remote sensing and field investigation methods. It resolved the complicated land surface characteristics, covered all aspects of factors influencing plant diversity, and possessed distinct spatiotemporal heterogeneities. The Yellow River Delta, the largest estuarine wetland in the northern China, was selected as the study area to demonstrate UEWGS in four seasons in 2017. A total of 123 species were recorded with considerable seasonal difference. Phragmites australis, Suaeda salsa, and Tamarix chinensis were the dominant species, and crop species also played important roles. In single effect, all aspects of gradients exerted significant influences, yet only vegetation gradient possessed significant influences in all seasons. In comprehensive effect, soil, vegetation, heat, and distance gradients showed significant gross influences. Moisture content in soil gradient and net primary productivity in vegetation gradient possessed significant net influences in all seasons and can be considered as the main driving factor and indicator, respectively, of plant diversity. The results validated the significance of UEWGS in revealing the plant diversity spatiotemporal characteristics and influencing factors, and UEWGS possessed universal applicability in the spatiotemporal analysis of plant diversity in estuarine areas.