This modeling study analyzes the simulated natural variability of pelagic ecosystems in the North Atlantic and North Pacific. Our model system includes a global Earth System Model (IPSL-CM5A-LR), the biogeochemical model PISCES and the ecosystem model APECOSM that simulates upper trophic level organisms using a size-based approach and three interactive pelagic communities (epipelagic, migratory and mesopelagic). Analyzing an idealized (e.g., no anthropogenic forcing) 300-yr long pre-industrial simulation, we find that low and high frequency variability is dominant for the large and small organisms, respectively. Our model shows that the size-range exhibiting the largest variability at a given frequency, defined as the resonant range, also depends on the community. At a given frequency, the resonant range of the epipelagic community includes larger organisms than that of the migratory community and similarly, the latter includes larger organisms than the resonant range of the mesopelagic community. This study shows that the simulated temporal variability of marine pelagic organisms' abundance is not only influenced by natural climate fluctuations but also by the structure of the pelagic community. As a consequence, the size- and community-dependent response of marine ecosystems to climate variability could impact the sustainability of fisheries in a warming world.