A small-scale mock-up test was carried out on a fractured hollow granite cylinder with compacted MX80 bentonite inside, to study the interaction between engineered barrier (compacted bentonite) and natural barrier (host rock with the presence of rock fracture). The swelling pressure and relative humidity of bentonite were monitored with respect to the position of the rock fracture during 349 days of infiltration. Herein, the variation of water content, dry density, suction and microstructure along bentonite column after dismantling were reported, focusing on the changes in the vicinity of the rock fracture, to evaluate the effect of the rock fracture on the swelling behaviour of compacted bentonite. Results showed that the presence of rock fracture disturbed the water content distribution, with a lower water content at a position closer to the fracture. A significant decrease in dry density was also observed in the vicinity of the rock fracture; the closer the positions to the fracture the larger the decrease of dry density. This decrease coincided with the reduction of swelling pressure recorded by the pressure sensors, suggesting the occurrence of rock fracture filling-up by bentonite. Further examination showed that when the soil suction was higher than 9 MPa, the decrease in dry density in the near field of rock fracture was mainly attributable to the increase in large pore porosity (>2 μm). This suggests that at this suction the mechanism involving intrusion of bentonite into the rock fracture with fracture width higher than the size of bentonite gains was related to the pushing effect under the swelling of bentonite behind. By contrast, when the suction became lower than 9 MPa, the bentonite gel formed from the exfoliation of clay particles might fill up the rock fracture with smaller aperture width.