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The advanced non-destructive method of neutron tomography, together with image analysis, is used to evaluate the structural evolution of an aggregated soil during one-dimensional compression tests. Aggregation of primary particles is a commonly observed phenomenon in natural and compacted soils that causes an open soil structure with two dominant pore sizes corresponding to macro (inter-aggregates) and micro (intra-aggregate) pores. The evolution of macro porosity and the degradation of structures are evaluated by means of morphological parameters such as volume fraction, size distribution and chord length. Change in the structure is then linked to the macroscopic soil response. It is observed that the major structural modifications are associated with irreversible strains in soil.