Deep geological repository is the preferred solution in many countries to manage radioactive wastes, such as in France where the Callovo-Oxfordian (COx) claystone is the candidate host rock. In such clay rock formation, the drilling of storage gallery creates an Excavation Damaged Zone (EDZ) with altered flow properties in the short term, while corrosion processes release large amounts of gas in the long term. Assessing the evolution of gas pressures in the near-field and predicting the effect of the EDZ on gas transport remains a major issue. This paper presents a second gradient two-phase flow hydro-mechanical (H2M) model tackling the multi-physics couplings related to gas transfers and fractures development. The EDZ is reproduced by shear strain localisation bands using a microstructure enriched model with a second gradient approach. The gas migration is captured by a biphasic fluid transfer model. The impact of fracturing on the flow properties is addressed by relating the permeability and the water retention curve to mechanical strains. Using this tool, numerical modelling of a drift in the COx claystone is performed with the aim of emphasising the influence of the HM couplings on gas migrations at nuclear waste disposal scale.