This study systematically investigated the pore structure response of kaolin and illite/smectite mixed-layer rich clay in a reconstituted state to one-dimensional (1D) compression by first performing oedometer tests on saturated clay slurries, followed by characterising their pore structure using multi-scale characterisation techniques, with the primary objective of advancing the current understanding of the microstructural mechanisms underlying the macroscopic deformation of such clays. Under 1D loading, the volume reduction observed at the macro level essentially represented the macroscopic manifestation of changes in inter-aggregate porosity at the pore scale. It was the inter-particle pores that were compressed, despite the interlayer pores remaining stable. Two distinct pore collapse mechanisms were identified: kaolin exhibited a progressive collapse of particular larger pore population in an ordered manner, whereas illite/smectite mixed-layer rich clay demonstrated overall compression of inter-aggregate pores. Accordingly, mathematical relationships between the porosity and compressibility parameters for these two soils were proposed, with the two exhibiting opposite trends arising from their distinct microstructural features. Approaching from the unique perspective of pore structure, quantitative analysis of pore orientation and morphology on the vertical and horizontal planes demonstrated some progressively increasing anisotropy during compression. These findings provide important insights into porescale mechanisms governing clay compression behaviour and enrich the limited microporosity database in soil mechanics.