Anthropogenic forcing caused the biodiversity loss and stability decline of communities. There is still controversy over whether the decline in biodiversity will lead to a decrease in community stability. The stability of biological communities is related to both biodiversity and structure, and this paper aims to reveal the human impacts on diatom communities' biodiversity and structure. We studied the richness, β-diversity and network distance of diatom communities in Qinghai-Xizang, Yunnan-Sichuan and Lower Yangtze River Basin, China through empirical dataset and simulation method. The results showed that the diatoms richness in the Qinghai-Xizang and the Yunnan-Sichuan region was lower and the network distance was higher than that of the Lower Yangtze River Basin. β-diversity in the Lower Yangtze River Basin was the lowest and the diatom network distance responds negatively to human population densities in China. The simulation showed that the network distance kept constant during random species loss, and declined while specialist species were lost or replaced by generalist species. The results suggested diatom communities' homogeneity and stability decline were associated with human activities. Human impacts may cause biodiversity loss targeted to specialist species or no biodiversity loss while generalist species replace those specialist species. This study showed that how diversity changes determined ecological stability depends on the type of species changes.