Warming climate impacts aquatic ectotherms both directly, by altering individual vital rates, and indirectly through environmental feedbacks and declines in body size, a phenomenon known as the temperature-size rule (TSR). However, understanding the relative importance of these effects in shaping community responses to environmental change remains limited. We employ a tri-trophic food chain model with size- and temperature-dependent vital rates and species interaction strengths to explore the role of direct kinetic effects of temperature and TSR on community structure along resource productivity and temperature gradients. We find that community structure, including the propensity of sudden shifts, is primarily driven by the direct kinetic effects of temperature on vital rates and thermal mismatches between the consumer and predator species, overshadowing the indirect effects through the TSR. Overall, our study enhances the understanding of the complex interplay between temperature, species traits and community dynamics in aquatic ecosystems.