Huanxiu Villa has driven a lot of research on its rockery because of GE Yuliang. Planting landscape, as an important landscape organization connecting the architecture, rockeries and water in the garden, has been ignored. This paper attempts to analyze the evolution of the plant configuration, design principle and scenery of Huanxiu Villa from the 18th century to the 21th century from the perspective of spatial morphology, combined with historical materials and field investigations. It’s discovered that the plants in the villa have undergone tremendous changes due to growth, aging, disease and death. After the replanting of the flowers and trees, their landscaping functions, appreciation methods and viewing seasons have also changed. Although the original planting method of flowers and trees is taken into consideration when replacing, the replaced plant morphology and growth characteristics make the composition of the planting landscape continue to evolve. The view of the landscape formed by replacing the rockery crape myrtle with black pine hides the perception of the south side of the rockery that was originally on the back of the mountain. The two clusters of palms that disappeared in front of the window of Buqiufang and on the rockery in the northeast concealed the innovation in the selection of species and the change in the concept of gardening in modern gardens. In modern times, the enclosed Fangshan pavilion surrounded by peaches, jujubes and papaya is the key to connecting the travel route space and enriching the sense of travel space. Nowadays, due to the disappearance of peaches and jujubes, it has become a semi-open space and the end of the travel route. The space of the villa is repeatedly reorganized in the unchanging landscape of rockeries, water and architecture, but evolving landscape of plant, changing visitors’ perception and understanding of space. Plant growth and the heritage protection guidelines that need to maintain their original appearance are mutually inconsistent. The resort’s measures to protect the rockery and pruning plants reflect that the protection of historical garden plants not only pays attention to the growth of individual plants, but also needs to take into account the relationship between plants and rockeries. It is enlightened that the protection of historical garden plant landscape needs to choose corresponding protection strategies according to the protection focus of different garden heritages.