In this study, a novel method for analysing inter-layer defects in slab tracks was proposed, based on fatigue analysis and the extended finite element method. The inter-layer gap of China Railway Track System (CRTS) II slab tracks was analysed. First, a finite element model was established to analyse the stresses in mortar layer under train and temperature loading. Secondly, the results of the stress analysis of the mortar layer were assessed using a fatigue analysis software for calculating the fatigue life of the mortar layer and the areas that fail first. Finally, in an extended finite element analysis, an initial gap was applied over the area that fails first, as determined through the fatigue analysis of the mortar layer. The patterns of the gaps at the ends, in the central part of the edge, and at the corner of the inter-mortar layer were observed and compared. Results show that the new method, which combines fatigue analysis and the extended finite element method, can address the discontinuity problem of the inter-layer slab defects in ballastless tracks, enabling the development process to be simulated. The rate at which the area of gapping increases can be used to characterize the development of the inter-layer gap in slab tracks.