To explore the current status of the Weishui Reservoir ecosystem and the ecological capacity of Hypophthalmichthys molitrix and Aristichthys nobilis, we used data from the fishery resource survey in July 2020 (summer), September 2020 (autumn), and January 2021 (winter) to establish an Ecopath model. The Ecopath model of the Weishui Reservoir consisted of 15 functional groups, and the fractional trophic levels ranged from 1 to 3.336. The keystones were Siniperca chuatsi and Culters, and the results indicated that their two niches, which included Hypophthalmichthys molitrix, Aristichthys nobilis, and Hemiculter leucisculus highly overlapped. The Finn cycling index (FCI), system connectance index (CI), and omnivory index (SOI) of the Weishui Reservoir were 11.35, 0.351, and 0.099, respectively, indicating that the Weishui Reservoir had a higher material recycling ratio than other lake and reservoir ecosystems, and that its functional groups had more closely and complexly connected relationships. The total system throughput (TST) of the ecosystem of the Weishui Reservoir was 44254.860 t/(km²·a), and the ratio of the total primary production to the total respiration (TPP/TR) was 1.394, indicating that the overall scale of the system was appropriate and was approaching a mature development stage. The biomasses of Hypophthalmichthys molitrix and Aristichthys nobilis in the Weishui Reservoir were 2.117 t/(km² ·a) and 16.577 t/(km² ·a), respectively, and their ecological capacities were 30.169 t/(km² ·a) and 236.217 t/(km² ·a), respectively.