To investigate the species composition, reproductive dynamics, and hydrological drivers of fish resources in the early stage in the Guiping section of the Xunjiang River, we conducted a two-year survey (2022–2023) downstream of the Datengxia Dam. A total of 22,464 fish eggs and larvae were collected, representing 6 orders, 17 families, and 67 species, with Cyprinidae (58.2%) as the dominant family. Dominant species included Squaliobarbus curriculus, Gobiidae, Hemiculter leucisculus, and Culter, exhibiting significant interannual variation in abundance. The breeding season peaked from May to September, accounting for 94.6% of annual recruitment. Hydrological conditions strongly influenced reproductive output: the multiple flood pulse periods in 2022 (peak discharge: 29,000 m³/s) yielded 34.997 billion eggs and larvae, whereas reduced flows in 2023 (peak discharge: 12,200 m³/s) led to a 75.4% decline (8.620 billion). Redundancy analysis (RDA) revealed that discharge, water temperature, natural hydrological data, and dissolved oxygen were the primary environmental drivers, explaining 46.11% of variability in larval abundance (p < 0.001). Notably, the proportion of important economic fish, “four major Chinese carps”, plummeted from 4.9% (2022) to less than 0.1% (2023), indicating spawning ground function degradation. Our results demonstrate that flood pulses are essential for sustaining fish recruitment, particularly for pelagic spawning riverine fish like the four major Chinese carps. Their proportion plummeted to less than 0.1% in 2023, highlighting the urgent need for eco-hydrological management in the Xunjiang River.