Field observations and theoretical modeling suggest that ongoing anthropogenic ocean warming will lead to marine ecosystem degradation. Mesopelagic fish are a fundamental component of the pelagic ecosystem, and their role in linking the surface- and deep-ocean ecosystems is essential for the biological carbon pump. However, their response to a warmer ocean is unconstrained because of data scarcity. Using extraordinarily well-preserved fish otoliths, we reconstruct a continuous mesopelagic fish community record in the Pacific Warm Pool region over 460,000 years. Fish production and diversity followed hump-shaped temperature gradients, with lower tipping point temperatures for the diversity than the production by ~1.5° to 2.0°C. During warmer-than-present interglacial periods, both production and diversity declined drastically. Our findings imply that the temperature-sensitive mesopelagic fish community at the southwestern margin of the Pacific Warm Pool, and possibly other hydrographically similar regions, may be especially affected if ocean warming continues unabated in the future.