This study investigated the diet compositions of Coreius heterodon and C. guichenoti in Yibin reach of Yangtze River from April to May, 2012 by carbon and nitrogen stable isotopes technique, and analyzed their diet relationship by the multivariate statistical technique, which covered the diet similarity index, overlap coefficient, and the influence of morphological differences in feeding organ between the two species on diet compositions. The results showed that, 1) the δ13C and δ15N of C. heterodon was from -21.15 per thousand to -20.31 per thousand and 9.67 per thousand to 10.21 per thousand, respectively, which indicated that the fish had an omnivorous possessing carnivorous preference. The δ13C and δ15N of C. guichenoti was from -23.30 per thousand to -21.18 per thousand and 7.40 per thousand to 9.21 per thousand, respectively, which had an omnivorous possessing phytophagous preference. There were some differences in the results between the stable isotopes and the traditional intestinal contents analysis. 2) The diet similarity index and the overlap coefficient was 78.7% and 55.6%, respectively. 3) The principal component analysis (PCA) result showed that the morphological characters of the feeding organs in the two fishes were different. In conclusion, the interspecies competition was not intense between the C. heterodon and C. guichenoti, and as the last investigation of the diet composition and food relationship of the two species before the impoundment of the Xiangjiaba Reservoir, the results could provide reference for analyzing the influence of impoundment on the fish trophic structure in Yibin reach of Yangtze River.