Water resource regulation is convenient for humans, but also changes river hydrology and affects aquatic ecosystems. This study combined a field investigation and two-dimensional hydrodynamic model (MIKE21) to simulate the hydrodynamic distribution from 1 March to 30 April of 2008–2013 and establish the HDI (habitat depth suitability index) and HVI (habitat velocity suitability index) based on static hydraulic conditions at typical points. Additionally, by using MIKE21 to simulate the hydraulic state in the study area under 20 flow conditions from 530–1060 m3/s, and combining these states with the HCI (habitat cover type suitability index), HDI, and HVI, we simulated the WUA (weighted usable area) and habitat connectivity under different runoff regulation scenarios to study the water requirements of Schizothorax during the spawning period in the Yanni wetland. The results showed the following: (1) the suitable cover type was cobble and rock substrate, with nearby sandy land; furthermore, the suitable water depth was 0.5–1.5 m, and the suitable velocity was 0.1–0.9 m/s. (2) Using the proximity index to analyse the connectivity of suitable habitats, the range of ecological discharge determined by the WUA and connectivity was 424–1060 m/s. (3) Habitat quality was divided into three levels to detail the flow demand further. When the flow was 424–530 m3/s or 848–1060 m3/s, the WUA and connectivity generally met the requirements under natural conditions. When the flow was 530–636 m3/s or 742–848 m3/s, the WUA and connectivity were in a good state. When the flow was 636–742 m3/s, the WUA and connectivity were in the best state. This study complements existing research on the suitability of Schizothorax habitat in Tibet, and introduces the connectivity index to enrich the method for calculating ecological water demand, providing a reference for resource regulation and the protection of aquatic organisms.