Chinese sturgeon (Acipenser sinensis) is an endemic, endangered and protected anadromous fish in China. This fish has been listed as a Category I nationally protected species in China and a critically endangered (CR) species of the International Union for Conservation of Nature (IUCN). Due to the restrictions by several special reasons of this species, e.g., long lifespan, complex migratory process, and precarious resource situation, it is quite difficult to objectively reveal the features of life history, and characteristics of distribution, and dynamics of habitat use (e.g., spawning/nursery site) by some traditional methods. Consequently, introducing more new innovative approaches is needed to achieve new breakthrough on research of migratory ecology and conservation for this species. In the present study, microchemical characteristics of three kinds of hard tissues of A. sinensis (i.e., otolith, dorsal scute, and pectoral fin ray) were studied comparatively by electron probe microanalyses (EPMA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) with their microstructure. The results show that otoliths of A. sinensis are loose in structure and contain small sand-like microcrystalline vaterite spherulites with independent core areas. In constrast, the dorsal scute is a stratified tissue while the pectoral fin ray is a relatively compact and uniform tissue. Viewed from the microchemical results of the three hard tissues, the analytical accuracy across all samples was high for Mg, Ti, V, Mn, Cu, Zn, Co, Sr, Ba and Ca with RSD<10%. The z-Scores of habitat element ratios for Co/Ca, Sr/Ca and Ba/Ca in both pectoral fin ray (-0.97-2.16, -0.78-2.56, -0.96-2.41) and otolith (-1.7-0.74, -1.24-0.98, -1.09-1.09) are consistent, while those z-Scores in the dorsal scute (-1.95-2.32, -1.68-2.03, -1.62-2.68) are fluctuative due to its stratification. At the same time, the microchemical maps of Sr, Ca and Ba in these three hard tissues revealed that pectoral fin ray and dorsal scute were uniform color/concentration while different parts of otolith showed different colors/concentrations. Based on the aforementioned findings and we consider practical needs from no lethality, difficulty of sampling and sample preparation process, tissular microstructure composition, and environmental element bioaccumulation. In the present study, the microstructure and microchemical characteristics of three kinds of hard tissues of A. sinensis, i.e., otolith, dorsal scute, and pectoral fin ray, were studied comparatively. The present study suggested that the pectoral fin ray is the best hard tissue material for microchemical study for reconstructing the history of the migration and life cycle of A. sinensis.