Endorheic rivers as landlocked systems with no hydrological connections to marine environments are suffering from water and ecosystem crisis worldwide, yet little is known about their structural characteristics with complex geomorphic and climatic dependence. Based on the river networks identified from 30 m resolution digital elevation models and surface water dynamic information derived from Landsat images, we investigate the hierarchical characteristics of 60 sub-basins in the Tarim Basin, the largest endorheic river basin in China. In the Tarim River basin, endorheic rivers exhibit a self-similarity only in the range of stream-orders 1–4, compared to the range of stream-orders 1–5 observed in exorheic rivers, owning to the limited stream power to maintain the similar aggregation of rivers in the arid regions. Moreover, the Tarim River networks demonstrate lower bifurcation ratio (2.48), length ratio (2.03), fractal dimension (1.38), and drainage density (0.24 km−1) in representative sub-basins, with a significant decay in median values compared with those derived from exohreic rivers at similar scales, suggesting sparser and imperfect developed branching river networks in endorheic basins. Further analysis on the Tarim reveals that endorheic river structure is more related to glacier extent (r = 0.67~0.84), potential evapotranspiration (r = 0.63~0.81), and groundwater type index (r = 0.64~0.73), which is essentially different from the structure of exorheic river represented by the Yellow River largely controlled by surface runoff, precipitation, and vegetation coverage. This study stresses the differences in intrinsic structural characteristics and extrinsic drivers of endorheic and exorheic rivers and highlights the necessity of differentiated strategies for endorheic river management in fragile ecosystems.