The dependence of hunter-gatherers on local net primary production (NPP) to provide food played a major role in shaping long-term human population dynamics. Observations of contemporary hunter-gatherers have shown an overall correlation between population density and annual NPP but with a 1,000-fold variation in population density per unit NPP that remains unexplained. Here, we build a process-based hunter-gatherer population model embedded within a global terrestrial biosphere model, which explicitly addresses the extraction of NPP through dynamically allocated hunting and gathering activities. The emergent results reveal a strong, previously unrecognized effect of seasonality on population density via diet composition, whereby hunter-gatherers consume high fractions of meat in regions where growing seasons are short, leading to greatly reduced population density due to trophic inefficiency. This seasonal carnivory bottleneck largely explains the wide variation in population density per unit NPP and questions the prevailing usage of annual NPP as the proxy of carrying capacity for ancient humans. Our process-based approach has the potential to greatly refine our understanding of dynamical responses of ancient human populations to past environmental changes.