Due to various factors such as installation, transportation, and irradiation non-uniformity, the centerline of the pellet in the fuel rod does not always completely coincide with the cladding’s centerline, resulting in a radial bias phenomenon of the pellet. Annular fuel, as an innovative new type of fuel with a geometric structure that features both inner and outer coolant channels. The annular pellets bias will have a non-uniform effect on heat transfer in both the inner and outer directions of the pellets. Further evaluation is needed to assess the impact of this phenomenon on the heat transfer performance of the annular fuel. In this study, an analytical model with original design dimensions and the begin of life annular fuel rods structure was established. Computational fluid dynamics (CFD) calculation methods were used to study the effects of different geometric structures of annular fuel on the fuel rod temperature field, thermal resistance, adiabatic surface position, and inwards or outwards heat transfer under no bias and five different bias rate. The results indicate that when annular fuel pellet bias appeared, changes in the pellet-outer cladding gap are opposite to changes in the pellet-inner cladding gap along the same angular direction, resulting in partially offsetting effects. Overall, pellet bias positively impacts the heat transfer performance of annular fuel. Additionally, the geometric structure of annular fuel significantly affects the heat transfer of the pellet, while the influence of pellet bias on heat transfer is relatively minor.