Resource polymorphism is a ubiquitous phenomenon in vertebrates and may represent a critical intermediate stage in speciation. Freshwater lakes in high‐altitude areas represent a natural system for understanding resource polymorphism in fishes benefiting from diverse lacustrine environments and species‐poor fish assemblages. We report resource polymorphism in a cyprinid fish, Schizopygopsis thermalis , in Lake Amdo Tsonak Co, a headwater lake in the upper Salween River system. Two discrete intraspecific morphs, planktivorous and benthivorous, were identified according to geometric morphometrics and traditional univariate linear measures. The planktivorous morph exhibits a longer head, longer upper and lower jaw, larger asymptotic standard length ( L ∞ ), lower growth rate ( k ), and higher growth performance index ( φ ) than the benthivorous morph. With respect to descriptive traits, the planktivorous morph possesses a large, terminal mouth and obvious mucus pores on the cheek and chin, while the benthivorous morph is characterized by a more inferior mouth with a sharpen horny edge on the lower jaw and unconspicuous mucus pores. The discrete pelagic–benthic resources and low interspecific competition in the lake system might drive the initial differentiation of the two morphs, and partial spatial reproductive isolation in breeding further maintains and reinforces the differences between them.