Otoliths are biogenic carbonate minerals whose microstructure and microchemistry have been used for age determination, stock identification, life history and environmental tracing. Using X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, we have determined the mineral types and crystalline characteristics of three pairs of otoliths from naked carp Gymnocypris przewalskii, the predominant fish in Lake Qinghai. The results indicate that the mineral of both lapillus and sagitta of the naked carp is aragonite, and that of asteriscus is vaterite. The aragonite of lapillus has prefect crystallization. Given the shape of lapillus and the sensitivity of its aragonite to water chemistry, lapillus was used to analyze temporal Sr/Ca ratios along the maximal growth axis by an electron probe microanalyzer (EPMA). Consistent variations of Sr/Ca ratios with a range of 1.0x10-3-5.0~10-3 on the long and short radii indicate that Sr/Ca ratios of lapillus potentially respond to the chemical compositions of the host waters during the period of the naked carp's growth and migration. Discontinuous (dark) zones of lapillus were formed during fall and winter when the naked carp grows slowly in Lake Qinghai, resulting in similar low Sr/Ca ratios to lake water, whereas incremental zones with higher St/Ca ratios respond to its migratory river waters during spring and summer. Various Sr/Ca ratios of incremental zones suggest that the migratory pattern of the naked carp may be much more flexible, rather than in a single river. Therefore, high-resolution otolith microchemistry of the naked carp can be used to trace its migratory behavior, which is of significance for determining its migratory pattern and life history of this precious species inhabiting the Tibetan Plateau.