Plinthite horizon (net-like soil horizon), as a part of the Quaternary red palesols, is believed to be an important record of the Quaternary paleoclimate and paleo-environment changes of subtropical areas in China. As an important part of the subsurface structure of red soil critical zone, plinthite horizon can harbor various bacterial communities, which may play key roles in mineral weathering and soil formation processes. Previous studies usually took the entire soil layer or genetic horizon as a single sample, while the intra-horizon differentiation of bacterial communities and co-occurrence network remain largely unknown. It is hypothesed that the plinthite horizon may affect the distribution of bacterial communities in the red matrix and white veins. Clarifying the characteristics of soil bacterial communities in plinthite horizon and its impact factors would help for exploring the biodiversity and understanding the multi-functionality of Red Soil ecosystems. By using the high throughput sequencing processes, the plinthite structure were here divided into two parts and the bacterial communities and their ecological networks under red matrix and white veins were analyzed. Results demonstrat that there is difference of bacterial composition between red matrix and white veins. Relative abundance of the phylum of Actinobacteria and Bacteroidetes are significantly higher in the red matrix of the plinthite horizon, while the relative abundance of Acidobacteria and Nitrospirae are significantly higher in the white veins. Bacterial ecological network and its topological features are also different between the red matrix and white veins in the plinthite horizon. Co-occurrence network (CoNet) analysis demonstrate that the ecological network of white veins contains more edges and has a lower network's clustering coefficient value. CCA analysis demonstrate that bacterial community composition and biodiversity in the plinthite horizon are caused by the environmental heterogeneity between the red matrix and white veins. Major element contents and particle size distribution are mainly impact factors that shape bacterial communities in the red matrix of the plinthite horizon.