Abstract: In order to evaluate food utilization and trophic transfer efficiency of the food chain in the Three Gorges Reservoir, stable carbon and nitrogen isotope methods were employed to investigate the spatiotemporal variations in the energy contribution of four fundamental carbon sources-phytoplankton, C₃ plants, C₄ plants in the riparian zone, and epiphytic algae-to four dominant small fish species, Squalidus argentatus, Saurogobio dabryi, Pseudobrama simoni, and Hemiculter leucisculus. The results indicated significant differences in the δ¹³C and δ¹⁵N values among different carbon source organisms, effectively distinguishing their fundamental carbon sources. The outcomes of the Bayesian mixed model suggested that phytoplankton contributes the highest proportion of energy to the four small fish species. At the hydrological scale, there is no significant difference in the contribution rates of autochthonous and allochthonous carbon sources to the four small fish (P>0.05). However, at the spatial scale, a highly significant difference was observed (P<0.01). This study indicate that autochthonous carbon is the primary energy source for small fish in the reservoir area, while the contribution of allochthonous carbon sources increases noticeably along the longitudinal gradient of the Three Gorges Reservoir. This may be associated with the characteristics of diverse submerged area and the increased sedimentation of exogenous carbon source particles in the quiescent water environment near the reservoir head.