Otolith is one of the most commonly used tools to trace fish life history, as its formation is affected by environmental factors during growth. This study investigates the otolith micro-chemical information of Schizothorax grahami from the upper (U1, U2, U3), middle (M1, M2, M3) and lower (L1, L2, L3) reaches in the source section of Chishui River, China, as well as the metal content of the water corresponding to fish habitats. Seventeen active elements in otolith were detected, and calcium (Ca) content was the highest (175605.4*10-6 g/g). Only strontium (Sr) was regularly distributed in otolith rings by face-scan images with a relatively small coefficient of variation. A paired two t-test showed that the values of Sr: Ca were significant differences among the samples from the three reaches through otolith line scans. In the correlation test after the first-order difference processing, the change frequency of Sr: Ca values in the otolith corresponded better to the line plots and significantly differed among the three reaches, especially the samples from the U3 and L2 sites. Therefore, analyzing Sr in the otolith of S. grahami from three reaches can differentiate fish stocks and reveal their unique life histories. The magnesium (Mg) in the otolith core at the early stage of fish life was significantly higher than that of the non-core area. Likewise, Mg content was higher in the fish spawning ground than in the non-spawning ground. Presumably, Mg content in the otolith was correlated to the water environment of the spawning ground. Meanwhile, the values of Mg: Ca in the otolith core showed significant differences among the samples from U3, L2 and the other sites, indicating that fish in these samples came from different spawning grounds. The characteristics of Mg in the otolith can reflect the life history of S. grahami in the Chishui River and the location of spawning grounds. This study indicates that strontium and magnesium in otolith can be used to trace the life history of S. grahami in the Chishui River and aid fishery management for different fish stocks.