Deep coral reef limestone, as the primary load-bearing medium in island-reef engineering, contains multi-scale pores whose internal development is a key factor causing strength degradation and making the failure characteristics of damaged zones difficult to predict. Based on high-resolution CT scanning and digital image analysis techniques, this study conducted three-dimensional structural reconstruction and parametric analysis of four typical structural types of deep coral reef limestone, namely framework, boulder, gravel, and calcarenite. The results show that pore volume, surface area, shape factor, and major axis length all exhibit right-skewed distributions, indicating a high frequency of small-sized pores, whereas meso- to macro-scale pores occur less frequently but exert a significant mechanical influence. The lengths of the three principal pore axes are highly positively correlated, suggesting that diagenetic processes such as erosion and dissolution shape pores through proportional enlargement or reduction. Based on the superposition criterion of pore-perturbed stress fields, a complex network model was established that simultaneously considers stress attenuation and pore size effects. Weighted degree and betweenness centrality were then used to identify the key pores controlling the mechanical properties, providing insights into the mechanism of mechanical deterioration in deep coral reef limestone.