Urban spatially morphological structure is the result of interaction between human activities and natural environment in specific geographical environment, and the formation and maintenance of urban biodiversity are the main ecological processes in urban space. Rapid urbanization leads to the increase of the intensity of land resources development and utilization, resulting in many ecological environment, social and economic problems. The "multiple plans integration" measure, put forward by relevant departments in the planning of land and space, is very important for effectively integrating the space planning and urban biodiversity conservation planning. In order to explore the internal relationship between spatially morphological structure and urban biodiversity in Karst mountainous cities, Anshun City, which is a typical karst mountainous city in Central Guizhou Province, was taken as the research object, and the spatial syntax and biodiversity related theories and methods were used to analyse the spatially morphological structure characteristics, plant species diversity characteristics and the coupling relationship between them. The results showed that:① The spatially morphological structure of Anshun City was strip distributed from southeast to northwest. On the overall level of the city, the characteristics of spatially morphological structure were as follows: the centrality was not obvious, the cores were scattered, the accessibility was poor, the degree of spatial connection was relatively weak, the regularity of network structure was not obvious, and the comprehensibility was unclear. ② The density of urban roads was low and unevenly distributed, and the densely areas were in the central urban and southwest area, with great traffic potential, high degree of spatial aggregation and good permeability. ③ The species diversity of plant community in Anshun city was low and different among different type green spaces, and from high to low in order of regional green space, park green space, attached green space, protective green space and square green space. ④ There was a significantly negative correlation between the spatially morphological structure and the species diversity of plant community on the overall level in Anshun City, in areas with high urban spatial morphological structure index, plant community species diversity was low, but this correlation was weak at the local scale. This study revealed the interaction between urban spatially morphology structure and biodiversity, and would provide theoretical basis for urban spatial planning, biodiversity conservation planning and maintenance. and would been important reference significance for the "multiple plans integration" approach in urban land space planning.