Abstract: X-ray Micro Computed Tomography (Micro-CT) is a non-destructive 3D imaging technique that plays a vital role in medical and biological research by enabling high resolution visualization and quantitative analysis of internal sample structures. This paper first elaborates on the structural composition, imaging principle, and experimental workflow of micro-CT, including key steps like sample pretreatment, parameter setting, data reconstruction, and data analysis. Secondly, it systematically reviews the application progress of micro-CT technology in fish research, covering multiple aspects such as whole-body tissue structure modeling of zebrafish, structure and evolution of bones (vertebrae, skull, pharyngeal jaw, teeth, etc.), lung evolution, otolith characteristics, cardiovascular development, skin and adipose tissue analysis, reproductive development tracking, and distribution of heavy metal accumulation. These applications demonstrate the unique advantages of micro-CT in qualitative and quantitative study of fish tissues. Finally, the paper points out existing issues in current micro-CT applications for fish soft tissue imaging, such as insufficient staining specificity, and provides an outlook on future technological development directions and application prospects. This review aims to offer references for promoting the in-depth application of micro-CT technology in ichthyological research.