The study of phylogenetic zones of plants provides a good insight into the biogeographic and ecological processes of zone formation and a clear understanding of the nature and origin of biodiversity hotspots. The literature in the Web of Science core dataset was analyzed using bibliometric methods combined with CiteSpace 5.0, VOSviewer 1.6.18 visualization software, and Excel software to reveal the characteristics, hotspots, and evolutionary trends of this field over the past 35 years. The research on plant phylogenetic systematics has been increasing at home and abroad, and the main research force is mainly in the United States. Among these research institutions, the Chinese Academy of Sciences has published more frequently than other institutions and conducted a considerable among of research in this field. The relevant research conducted in this field is mainly focused on ecology, with significant interdisciplinary characteristics and the closest connection between ecology and other disciplines. The hotspot research topics at each stage are closely related in the field of plant phylogenetic systematics. These topics at each stage have a strong knowledge transmission relationship in the field of plant phylogeny and show a trend of further development based on the original foundation. In the future, the cross-fertilization of disciplines will be further promoted to realize the following objectives: strengthen mechanistic studies, combine different research methods of phylogenetic tree construction and model prediction in different phyla, understand the dynamic changes of plant communities, ecosystems, and global scale biodiversity from new perspectives, and provide the scientific basis for effective conservation of species and clarification of the evolutionary history and formation mechanism of phyla. Thus, it is still a popular research direction in the field of plant phylogenetic systematics.