Abstract: To explore the physicochemical characteristics, stability and bioavailability of two geometric isomers of astaxanthin encapsulated by nano-emulsion, in this study, all-E astaxanthin nano-emulsions (all-E-AST NEs) and Z-astaxanthin nano-emulsions (Z-AST NEs) were prepared through high-pressure homogenization. The physicochemical characteristics of the two nano-emulsions were compared using a particle size analyzer, colorimeter, ultraviolet-visible spectrum, infrared spectrum, and scanning electron microscope. The stability of the nano-emulsions was evaluated under a range of conditions, including heating, illumination, and storage. Moreover, the diffusion model method was employed to assess the bioavailability of astaxanthin isomers. The results demonstrated that the appearance colors of the all-E-AST NEs and Z-AST NEs were pale pink and orange yellow, respectively. Compared with all-E-AST NEs, the L^*, a^* and b^* of Z-AST NEs were significantly increased (P<0.05), the average particle size and polydispersity index (PDI) were observed to decrease by 30 nm and 0.043, respectively. In addition, the encapsulation efficiency was markedly enhanced by 6.1% (P<0.05), and the Z-AST NEs exhibited heightened ultraviolet absorption. The micro-morphology of the two nano-emulsion powders exhibited notable disparities, contingent on the high crystallinity of all-E-astaxanthin and the amorphous state of Z-astaxanthin. Furthermore, the stability of all-E-AST NEs under high-temperature, illumination and long-term storage conditions was significantly higher than that of Z-AST NEs. Meanwhile, the partition factor of Z-AST NEs was 3.54 times that of all-E-AST NEs (P<0.05). Collectively, the findings of this study demonstrate that there are notable differences in physicochemical characteristics between all-E-AST and Z-AST NEs. The former exhibits superior stability, while the latter displays higher bioavailability. These observations provide theoretical guidance for the application of astaxanthin geometric isomer nano-emulsions in healthy food.