Population patterns of deep-sea fauna reflect interacting physiological and ecological drivers, yet the mechanisms structuring these patterns remain poorly resolved due to historically low sampling resolution. This has limited our understanding of species’ true bathymetric ranges and constrained our ability to assess deep-sea ecosystem structure. Amphipods are an abundant, diverse, and readily sampled macrofauna that provide an effective model system for resolving these processes across depth gradients. Here, we present a high-resolution dataset from the Nova Canton Trough, Central Pacific Ocean, where 114 free-fall landers recovered 139,431 amphipods from between 2,751 to 7,983 m using baited traps. Twenty-seven species were identified using integrative taxonomy, enabling detailed analysis of bathymetric distributions. Six abundant species spanning abyssal and hadal environments were selected for population structure analyses using instar proportions and body-length frequency via Kernel Density Estimates. Hadal species exhibited clear ontogenetic vertical structuring (OVS), with juveniles dominating depths between 6,000-7,500 m, and adults occurring below 7,500 m. Whereas abyssal taxa showed no such pattern. This represents the first evidence of OVS outside subduction trench systems and suggests that life-history stage plays a key role in structuring hadal amphipod populations. These findings demonstrate the value of amphipods as model organisms for resolving fine-scale biological processes in the deep sea. Improving our understanding of population structure and species depth limits is critical for predicting connectivity between deep-sea features, predicting species responses to disturbance, and therefore informing environmental assessments and sustainable governance of deep-sea ecosystems.