To reveal the effects of different fertilization modes on the pore structure of paddy soil in Guangxi, four treatments were selected as the research objects: CK (no fertilization), CF (winter fallow + conventional fertilization + straw removal), OPT (winter fallow + optimized fertilization + straw removal), and GM (winter green manure + optimized fertilization + straw return). X-ray computed tomography (CT) technology, combined with image analysis, was used to quantitatively characterize the two-dimensional characteristics and three-dimensional structure of soil pores under different treatments, and three-dimensional reconstruction and visualization of the soil pore structure were performed.The results showed that the CK treatment had the highest number of both small pores and total pores, but these existed mostly as independent and ineffective micropores, exhibiting typical characteristics of soil degradation. The CF and OPT treatments did not show advantages in the number of medium-large pores or total pore volume; however, three-dimensional indicators such as porosity, connectivity, and branch density showed some improvement compared to CK. The mean surface density of GM showed no significant variation across different soil layers, in contrast to the other treatments where it gradually decreased with increasing soil depth. In terms of three-dimensional pore size distribution, the number of medium-large pores in the GM treatment was significantly higher than in the other treatments. Moreover, three-dimensional indicators such as porosity, specific surface area, connectivity, and branch density were all greater in GM than in the other treatments. In the three-dimensional reconstruction images, the pore structure of GM was densely and uniformly distributed within the main root growth zone of rice, significantly outperforming the other treatments.The study demonstrates that the application of chemical fertilizers alone is insufficient to construct an ideal, well-connected pore structure. In contrast, the combination of winter green manure cultivation with straw return can better establish an optimal soil pore structure, which is conducive to rice root growth and thereby enhances crop yield.