The assessment of masonry structures is more and more useful to characterize the behaviour of masonry walls, tower and bridges. The owner of these constructions would like to understand the mechanical performance of their structures. Experiments and computational methods are two essential elements to accurately study and determine the sensitive points of the edifices. This paper presents the numerical modelling of a vault in undamaged and damaged domain with a macro-homogenisation analysis. The importance of considering the building phases in order to determine the actual stiffness of the structure is highlighted. The numerical tool is a continuous finite element model based on an original anisotropic damage model considering the masonry as a homogenised continuous media. The model is implemented in a massive finite element for three dimensional formulation. It computes the localized damage and allows indicating zones of privileged crack opening in the structure. It is able to predict the cracking zones in large masonry constructions without pre-positioning joint elements. It uses a regularization method ensuring an independence of the numerical response from the mesh. The model includes also a re-closure function for cracks. This re-closure function allows simulating the progressive stiffness restitution during the crack re-closure process. The paper focuses on this aspect in relation with the crack induced by restrained shrinkage of joint mortar during the building history. First, a state of the arts is proposed, then the damage model is presented. In order to validate the model and to propose a global methodology, the damage model is applied to analyse a thin masonry vault previously tested in a laboratory. The numerical results are discussed regarding the experimental ones.