[Objective] In this study, the main goal was to explore the spatial heterogeneity and driving factors of soil microbial populations from Chlorobi phylum in different vegetation zones from the middle reach of Xilin River Basin. [Methods] We selected the typical riparian vegetation zones along the landward direction from the riverbed center (BC) without vegetation zone to the river terrace. These vegetation zones included Juncellus serotinus-dominated marsh plant communities from riverbed side (BS), Juncus effusus-dominated marsh meadow plant communities from low floodplain (LF), Potentilla anserina-dominated meadow plant communities from high floodplain (HF), Leymus chinensis grassland on the river terrace (LT) and Stipa grandis grassland on a slope in the hilly zone (HT). Meanwhile, we collected 0-10 cm soil samples and analyzed the spatial distribution characteristics, abundance and composition of soil Chlorobi communities based on 16S rRNA gene high-throughput sequencing. To explore the environmental factors driving the spatial heterogeneity of soil microbial communities from Chlorobi phylum, we detected the soil physiochemical factors.[Results] Nine populations from the orders Chlorobiales and Ignavibacteriales were detected at genus level. The highest relative abundance of Chlorobiales1, Chlorobiales2, Chlorobiales6, Ignavibacteriales7 and Ignavibacteriales9 were less than 0.40%, while those of the other four populations from order Ignavibacteriales ranged from 0.54% to 1.06%. The relative abundances of both Chlorobiales1 and Chlorobiales2 in HF, LT and HT were higher than those in BS (P<0.05). The abundance of Chlorobiales1 was significantly positively correlated with pH and total organic carbon content (P<0.01), while that of Chlorobiales2 was significantly positively correlated with the content of clay and silt particles (P<0.01). The relative abundances of Chlorobiales6 and Ignavibacteriales8 in BS were higher than those of the other vegetation zones (P<0.05). Their abundances were significantly positively correlated with ammonia nitrogen content (P<0.01). Variation partitioning analysis (VPA) showed that soil water content accounted for 65.7% of the spatial variation of microbial communities from Chlorobi phylum. [Conclusion] In the Xilin River Basin, the populations of Chlorobi communities from different vegetation zones demonstrated obvious spatial heterogeneity. Water content was the main driving factor of the spatial heterogeneity of the soil microbial communities from Chlorobi phylum in different vegetation zones.