[Background] Complete and incomplete nitrification driven by Nitrospira plays a key role in global nitrogen cycle, but little is known about the niche differentation of Nitrospira, and associated environmental driving forces for Nitrospira’s niche separation and as well as possible functions like complete nitrification driven by Nitrospira in Xilin river basin. [Objective] To reveal the niche differentiation of Nitrospira and associated environmental driving forces, and deciphering the possible functions like complete nitrification driven by Nitrospira. [Methods] Based on high throughput sequencing of 16S rRNA gene with bioinformatics analysis, the compositions and abundance of sediment/soil Nitrospira populations were analyzed. Meanwhile, their niche differentiation and associated environmental driving forces were characterized so as to predict their potential complete nitrification. [Results] Nine Nitrospira genera were detected, of which Nitrospira 1, 2 and 4 were dominated in xeric environment, which were negatively correlated with sand, water content, pH and ammonia nitrogen (AM) while positively correlated with nitrate nitrogen (NR), dissolved salt (DS), total organic carbon (TOC), total nitrogen (TN), total phosphorus (TP), silt and clay contents. In comparison, Nitrospira 5, 6, 7, 8 and 9 were dominated in aquatic and hygric environments, positively correlated with sand content (except Nitrospira 9 negatively correlated with AM), etc. and negatively correlated with silt content, etc. Interestingly, Nitrospira 3 was preferentially distributed in the center of the river bed with aquatic environment, only positively correlated with sand and silt contents, but negatively correlated with the other environmental factors. [Conclusion] There was obvious niche differentiation of Nitrospira populations with a wide range of habitat adaptability in Xilin river basin. Nitrospira 1, 2 and 4 were most suitable to colonize xeric environment with relatively rich nutrients, positively driven by silt content, etc. Whereas Nitrospira 5, 6, 7, 8 and 9 were most suitable to inhabit relatively oligotrophic aquatic and hygric environments, positively driven by sand content, etc. Nitrospira 3 preferred silt, free water and low ammonia in oligotrophic aquatic environments, positively driven by only sand and silt contents. Briefly, silt content, dissolved salt (DS) and ammonia nitrogen (AM) were the main environmental driving forces for niche differentiation of Nitrospira groups. So i) Nitrospira 3 was presumed as probable comammox; ii) the other Nitrospira populations like 1, 2, 4, 5, 6, 7, 8 and 9 belong to comammox remains to be further discussed.