The Shichuan River is a primary tributary of the Weihe River and the largest tributary of the Yellow River, which flows through the northern part of the Guanzhong Plain in Shaanxi Province. This region is characterized by a delicate and complex ecological environment. We conducted systematic aquatic ecological investigations on four rivers in the Shichuan River Basin in February 2022 (winter), May 2022 (spring), August 2023 (summer), and November 2023 (autumn). A total of 148 benthic macroinvertebrate species were recorded. The number of species followed the pattern of spring (85)>autumn (71)>winter (56)>summer (47). The average density (ind·m) was in an order of autumn (91.2)>winter (88.9)>spring (53.9)>summer (41.9). The average biomass (g·m) exhibited autumn (2.8)>winter (0.8)>spring (0.5)>summer (0.4). By conducting distribution range tests, discriminant analysis, and correlation analysis on 26 parameters of benthic animals in four seasons, we constructed a benthic integrity index (B-IBI) for the Shichuan River Basin. Subsequently, we evaluated the B-IBI health of 20 sampling points (5 reference points and 15 damaged points) which presented significant spatiotemporal variations in the biological integrity. The number of sampling points in a sub-healthy or healthy state in the Shichuan River Basin was in an order of autumn (13)>summer (11), winter (11)>spring (9), with the health condition being the best in autumn. Spatially, the number of sampling points in a sub-healthy or healthy state in the mountainous section (29) was greater than that in the plain section (15), and the health condition in the mountainous section was the better. Environmental factors affecting benthic community structure in all seasons included water depth, flow velocity, total phosphorus, ammonium nitrogen, conductivity, water temperature, dissolved oxygen, silicon, nitrate nitrogen, total nitrogen, and total dissolved solids. Our results could provide support for the ecological management and restoration of benthic macroinvertebrates in the Shichuan River Basin.