Northern tropical karst seasonal rain forest, located on the northern margin of the tropical limestone karst region of China, is unique in the world and represents one of the world’s most remarkable types of karst forest. The limestone karst forests in this region display various characteristics, such as a variety of community structures, high species richness, and abundant endemic biological species, owing to the special limestone soils with abundant Ca and relatively high pH, the variety of heterogeneous habitats, and the impacts of the monsoon climate. An approach to the analysis of species composition and spatial distribution based on the investigation of a permanent plot is fundamentally important for revealing mechanisms of biodiversity maintenance in this area. The 15 ha Nonggang Northern Tropical Karst Seasonal Rain Forest Dynamics Plot (22.43°N, 106.95°E) was established in 2011. The plot is located in the Nonggang (or Longgang) National Nature Reserve in Guangxi, southern China, adjacent to northeastern Vietnam. Based on the standard field protocol of the Center for Tropical Forest Science (CTFS), all free-standing individuals in this plot with DBH (diameter at breast height)≥1 cm were tagged, mapped and identified to species. The results of the study were as follows: (1) A total of 95,471 individuals, including trees with multiple trunks, belonging to 223 species, 157 genera and 56 families were recorded in the plot. (2) Community composition, both at the family and the generic level, was dominated by tropical floristic elements. The most dominant families were Euphorbiaceae, Verbenaceae, and Moraceae. (3) The 11 species with the greatest numbers of individuals represented 51.64% of the total individuals, and the 58 species with the greatest numbers of individuals represented 90.19% of the total individuals in the plot. Seventy-five species were considered to be rare species because they were represented by no more than one tree per hectare, accounting for 33.63% of the total species. (4) The DBH size-class structure of all species in the plot exhibited a reverse J-shaped pattern, indicating good regeneration across the community. (5) Species composition exhibited strong spatial variation in the plot. The strongly drought-resistant Boniodendron minus and Memecylon scutellatum were the dominant species on the mountain peaks. Excentrodendron tonkinense and Cleistanthus sumatranus were the dominant species on the middle slopes. The strongly shade-tolerant Erythrina stricta and Ficus hispida were the dominant species on the valley bottoms. (6) The trees with DBH>20 cm showed a higher density in the valley bottoms, whereas the trees with DBH between 10 and 20 cm were distributed evenly over the entire plot. The individual trees showing ramifications and the tree sprouts showed a higher density on the mountain peaks. (7) The species–area relationship scatter diagram consisted of two curves for sampling areas ranging between 2 and 7 ha, indicating strong spatial heterogeneity of species composition in the plot. The study suggested that the strong habitat heterogeneity and the special geological background of the area may be important for regulating the species composition and spatial distribution of trees in this karst seasonal rain forest.