The tritium breeding pebble bed is a core component of the fusion blanket, in which the tritium purge gas flows through. Its flow and heat transfer characteristics are crucial for achieving tritium self-sufficiency and ensuring safety operation of blanket. The internal heat source generated by tritium-producing nuclear reactions significantly impacts the flow and heat transfer in the pebble bed. This study investigates this impact in a lithium silicate pebble bed within the China Fusion Engineering Test Reactor, focusing on non-uniformly distributed heat sources. A numerical analysis coupling Discrete Element Method and Computational Fluid Dynamics was used to compare the thermal–hydraulic characteristics (flow field, temperature field, and pressure field) with and without internal heat generation. Results indicate that the variation in average flow velocity along the x-direction correlates with the porosity distribution along the same direction within the pebble bed. Furthermore, the purge gas velocity increases with the addition of internal heat sources due to the temperature rise and consequent density reduction of the heated gas. Besides, internal heat sources intensify local thermal non-equilibrium effects between the gas and solid phases. Finally, the pressure drop increases with internal heating due to the increased viscosity of the tritium purge gas.