Understanding resource partitioning between species is crucial to describe the coexistence mechanisms between them, and to reveal the ecological functions they serve in ecosystems. Among existing approaches, functional morphology is widely used in aquatic animals, such as phytoplanktons, invertebrates, and fish, by explaining their foraging and swimming characteristics in water bodies. However, little attention has been paid to tadpoles, which may have important functional roles in freshwater ecosystems. Therefore, a functional approach was used, and three indices (i.e., functional richness, functional identity, and functional overlap) were calculated in the present study to reveal the coexistence mechanism between Leptobrachium boringii and Quasipaa boulengeri tadpoles in Heilongjiang Stream of Qingyinge, Emei Mountain. Our results indicated that the observed functional richness of L. boringii tadpoles (12.59%) was lower than that of Q. boulengeri tadpoles (46.67%). Upon randomly selecting 15 and 51 individuals from the two tadpole populations (L. boringii and Q. boulengeri, respectively), the functional richness of L. boringii was observed to be significantly lower than that of Q. boulengeri. Moreover, functional identity was significantly different between the two tadpole species based on PERMANOVA analyses (P<0.001). In addition, functional overlap between the two tadpole species was extremely low in both observed (1.47%) and bootstrap values (mean=0.06%±0.19% SD when 15 individuals were randomly selected; and mean=0.99%±0.55% SD when 51 individuals were randomly selected). All of these results suggested the existence of niche differentiation between the two tadpole species. Specifically, L. boringii tadpoles displayed larger bodies, smaller mouths, larger interocular distance, stronger tails, and their swimming types were some dorso-ventral flexion, with little lateral flexion. In contrast, Q. boulengeri tadpoles can have larger mouths, smaller interocular distances, smaller tails, and swimming behaviour were altered due to greater magnitudes of vertebral curvature. Since functional traits can be correlated with micro-environmental factors, habitat differentiation could also be expected between the two tadpole species.