Underwater drilling and blasting are widely used in current aquatic engineering. The shock waves generated by blasting exhibit high instantaneous intensity and rapid diffusion, raising significant concerns about their impact on aquatic organisms and ecosystems. Due to their small size and limited swimming escape capacities, drifting larvae are particularly vulnerable to underwater shock waves represent a key focus of concern. Using grass carp (Ctenopharyngodon idella) larvae as the object, the damage threshold and mechanism were revealed through field blasting experiments (single-hole charge of 26 kg, total charge of 300 kg) combined with laboratory cultivation and histological analysis. The results indicate that when the peak shock wave pressure decreases to 0.383×10⁵ Pa (corresponding to a distance of 500 m to the blasting center), the instantaneous mortality rate after 4 days of cultivation become comparable to those of the control group (P>0.05), establishing 500 m as the ecological safety distance for grass carp larvae. Histological analysis demonstrates that the damage to liver tissue caused by shock waves exhibits distance-dependent characteristics, with renal injury identified as the core factor contributing to delayed mortality. The glomerular structures remain largely intact in the ≥200 m group, but the 300 m group still shows an 18.9% risk of sublethal damage. Considering the hydrological characteristics of the upper Yangtze River and the distribution of protected areas, precise control of underwater blasting parameters combined with millisecond-delay blasting technology can significantly reduce shockwave intensity and affected range. A comprehensive protection strategy was proposed, which included strict avoidance of breeding seasons (May—July), application of rapid-flow-adapted double-layer bubble curtains, and establishment of a compensation mechanism involving “real-time monitoring and stock enhancement releases”. The research results have clarified the quantitative damage thresholds and mechanisms for grass carp larvae, which can provide scientific basis for the coordinated high-quality development of water-related engineering projects (such as waterway regulation in the upper Yangtze River) and aquatic ecological conservation.