Sand media filters are often among the common filter modes in micro-irrigation system due to its excellent fouling capacity. The sand filter intercepts impurity particles mainly through the filter layer pores. The pore structure of filter layers directly affects the effect of particle deposition and transport during filtration .The objective of this work was to to master the internal pore structure characteristics of sand filter layers composed of different granular filter media. Taking ordinary Quartz Sand(QS1), Sea Sand(SS2), ASM Modified Glass(MG3) and Glass Beads(GB4) with selected grain size1.0~1.18 mm as research objective, this study employs the advanced CT scanning technique to construct the three-dimensional(3D) structure of four filter layers. In combination with image analysis software VGStudio MAX, Image J, et al, the pore structure parameters such as porosity, pore size distribution, pore roundness value and flatness ratio of four filter layers were obtained by processing different filter layer CT slices. In order to investigate the complexity of different layer pore structure, the box-counting fractal dimensions of pore structures were calculated with fractal theory. The research results showed that the apparent porosity range of the four filter layers were 39.7%-44.6% (QS1), 38.5%-42.3%(SS2), 40.7%-45.6%(MG3), 34.8%-38.7%(GB4) and the volume porosities were 42.2%, 41.2%, 44.1%, 36.6% respectively. The pore size intervals were 75-960, 80-760, 70-1 050, 85-930 μm and the difference was not significant. The calculated pore roundness value ranges were 1.59-1.78, 1.35-1.54, 1.65-2.03, 1.20-1.36, the pore flatness ranges were 2.62-2.75, 2.05-2.20, 3.04-3.21, 1.94-2.04, the fractal dimensions Db of the four filter layers were 1.621, 1.566, 1.661 and 1.446, respectively. This study quantitatively characterized the pore structure characteristics of the filter layer, and obtained the differences of meso-pore structure of different granular filter media. The apparent porosities of the top filter layers were more higher than that of the bottom layers along the depth of the filter. The pore size distribution law was that small pores (<75 μm) accounted for the majority for all the four granular media and the pore shapes were mainly narrow and long type. With the media particle angularity increase, the distribution of the apparent porosity was more dispersed and the volume porosity was higher, the proportion of macro-pores increased accordingly and the maximum value reached 17.24% for MG3. The tendency of pore shape parameters deviation from sphericity was more obvious. The fractal box-counting dimension, which represented the complexity of pore structure, increased with the media angularity accordingly, and fractal dimension was negatively correlated with apparent porosity. The quantitative analysis of filter layers pore structure can overcome the shortage of traditional model experiment and provide a foundation for the subsequent study of particle deposition and migration in the filter layers.