Ceratoscopelus warmingii, a common mesopelagic fish in cold seep ecosystems, plays a crucial role in transferring energy and materials between different water layers, thereby influencing deep-sea carbon cycling and storage. In August 2023, we collected samples from four depths (75 m, 400 m, 500 m, and 600 m) in cold seep waters to analyze the trophic niche characteristics of C. warmingii using stable isotope techniques. The results indicated significant differences in δ13C and δ15N values among the water layers, with mean δ13C and δ15N values of −19.85 ‰±0.33 ‰ and 8.41 ‰±0.62 ‰, respectively. Indicators of trophic structure showed distinct vertical differentiation, with the width of the trophic niche decreasing as depth increased. At 75 m and 400 m, the consistency of CR and NR indicators and high trophic niche overlap indicated similar food sources, confirming vertical migration behavior. In contrast, at 500 m, the MNND and SDNND values suggested a more stable trophic structure, while at 600 m, changes in feeding sources pointed to a distinct population. The Standard Ellipse Area of Overlap (SEAc) was highest between 75 m and 400 m, while the divergence of trophic ecological niches at 600 m, with different food sources, suggests that cold seep ecosystems at this depth provide a relatively stable trophic structure for C. warmingii and support the formation of an independent population. In cold seep ecosystems, C. warmingii employs adaptive trophic strategies to optimize survival under varying habitat conditions at different depths. This vertical trophic differentiation reduces intraspecific competition and enhances population stability in deep-sea habitats. This study enhances our understanding of the trophic niche and vertical migration of C. warmingii in cold seep ecosystems, significantly contributing to our knowledge of biodiversity, energy flow, and material cycling in these unique environments.