Calcareous sand, also known as bioclastic deposits, has distinct composition and morphological characteristics compared to siliceous sand. The exploration of the South China Sea has revealed a high potential for slurry pressure balanced (SPB) shield tunnelling in coastal areas that pass through calcareous sand strata. However, the impact of the differences between calcareous sand and siliceous sand on filter cake formation remains unclear. This study aimed to investigate the slurry infiltration characteristics of calcareous sand and siliceous sand (with Fujian sand as a representative) with the same permeability coefficient through micro slurry infiltration column tests. The macroscopic differences in slurry infiltration between the two media were observed. The sand columns were scanned before and after slurry infiltration using a CT scanner, allowing for the reconstruction of both the original particles’ topology and the pore network of the sand column. A pore network model was established, and the Dijkstra algorithm was used to identify the dominant particle infiltration paths, with flow resistance serving as the weight criterion for evaluating pore connectivity performance. The study found that the differences in particle topology and connectivity of the pore network were the fundamental mechanisms underlying the macroscopic slurry infiltration behaviors between different types of sands. These differences also explained the influence of particle size on the slurry infiltration characteristics for the same type of sand. The findings shed light on the fundamental mechanisms driving the differences in slurry infiltration behaviors and provide insights into the influence of particle size on slurry infiltration characteristics within the same type of sand.