This paper investigates the swelling behaviour of compacted MX80 bentonite under hydration with the presence of initial voids that simulate the technological voids in real nuclear waste repositories. With water introduced into samples from the initial voids, the swollen bentonite first filled up the initial voids, and then swelling pressure was generated. At different hydration times, the microstructure was investigated at different heights (initial void, top, middle and bottom) using mercury intrusion porosimetry, together with the determination of dry density, water content and suction. It was observed that the microstructure was characterised by the presence of a large- and a small-pore families at bottom and middle layers, but by the creation of a new medium-pore family with dominant pore mode around 0·04–2 μm at the top and initial void layers after the void space was filled by swollen bentonite. From bottom to void, the significant increase in medium pores was accompanied by an increase in inaccessible pores and a decrease in large and small pores. Further examination showed that the sample could be divided into compression and swelling zones based on the variation of void ratio with swelling pressure: at the compression zone, the soil was compressed over time, characterised by a significant reduction of medium and large pores; whereas at the swelling zone, the soil was still undergoing swelling, represented by the increase of inaccessible pores and medium pores. In addition, the changes in microstructure along the sample were found to be well correlated with changes in dry density and water content: the water content was decreasing and the dry density was increasing from the initial void to the bottom positions; over time the dry density of the upper part was increasing due to compression, while the dry density of the lower part was decreasing due to swelling. This provided evidence for the main mechanism of compacted bentonite swelling with the presence of technological voids: the swollen bentonite fills the initial voids first and then undergoes compression by the swelling of the bentonite behind.