The development of a high-grade waterway network in the Upper Yangtze River will play a crucial role in promoting the economic and social development in the Chengdu-Chongqing region. Waterway improvement through underwater blasting to removal the obstructing rocks is still one of the most effective method in mountainous river management, but its impact on aquatic organisms, particularly on passively drifting fish eggs and larvae, has raised significant ecological concerns. Long-term observational data of drifting larvae in the Upper Yangtze River were analyzed, focusing on their temporal distribution patterns and spatial variations in species composition and abundance. The propagation mechanisms of underwater blasting shock waves were examined, and the primary factors affecting shock wave intensity were identified. Current research on blast-induced fish damage was reviewed, with special attention paid to the effects of shock waves on eggs and larvae. Based on the documented drift patterns of eggs and larvae and the characteristics of shock waves, comprehensive ecological protection measures were proposed. These measures included temporal and spatial avoidance strategies, optimized blasting techniques, and the use of bubble curtain technology. These findings provide valuable insights for achieving sustainable development that balances waterway construction with ecological conservation in the Upper Yangtze River.