The biodiversity value of river-oxbow lake systems in high plateau peatland has been little recognized, and there are many gaps in our understanding of their ecology. In this study, we investigated the river-oxbow lake system of the Bai River basin, the main tributary of the Yellow River Source in the Zoige wetland from 2015 to 2016, in attempt to show how the environmental variations, especially hydrological connectivity and macrophyte biomass in the river-oxbow lake system influenced macroinvertebrates. Habitat patches were investigated in 11 river cross-sections and 18 oxbow lakes in the Bai River basin. Through hierarchical clustering and non-metric multidimensional scaling, four main types of habitats were identified in the river-oxbow lake system in the plateau: sand-bed river, cobble-bed river, sparse-macrophyte oxbow lake, and luxuriant-macrophyte oxbow lake. The luxuriant-macrophyte oxbows were characterized by high dissolved oxygen concentrations, alkalinity, and higher macroinvertebrate richness, density, biomass, and the Improved Shannon-Wiener Index in comparison to the other habitat types. Additionally, influential patterns of environmental variables on macroinvertebrates were analyzed using redundancy analysis. Lasso regression models were established to describe how macroinvertebrate density responded to macrophyte biomass and other variables, and how macrophyte biomass responded to hydrological connectivity and oxbow size. It was revealed that reduced hydrological connectivity and reduced oxbow size played important roles in increasing the biomass of submerged macrophyte, and dense macrophyte was directly responsible for the high biodiversity of macroinvertebrates. Different from the commonly believed unimodal influential pattern that medium hydrological connectivity supports the highest biodiversity in oxbow lakes reported in previous studies, macroinvertebrates in the high plateau river-oxbow lake systems benefited from low connectivity and reduced size. Oxbow lakes, especially those covered with luxuriant macrophytes, diversified the macroinvertebrate assemblages and enhanced primary consumer biomass at the regional scale.