Abstract: For the rock masses with non-persistent joints under loading in engineering structures, two conceptions are put forward, which are the loaded microscopic damage and the macroscopic damage with joints. Defining the initial damage state of intact rock as the basic state, considering the existence of macroscopic defect with joints, the damage propagation of microscopic defects, micro cracks and the coupling action of macro and micro defects under loading, the compound damage variable (tensor) is deduced based on the Lemaitre strain equivalence hypothesis. The formula for calculating the macroscopic damage variable (tensor) is given, then the three-dimensional damage constitutive model for the rock masses with non-persistent joints under loading is established based on the coupling of macroscopic and microscopic defects. Finally, the test data are adopted to validate this model, and the effects of macro and micro-defects on the mechanical properties of fractured rock masses under different confining pressures are discussed. The research results show that: (1) The mechanical properties of rock masses under loading in engineering structures are determined by the loaded microscopic damage, macroscopic damage with joints and stress state of rock masses. The mechanical properties of rock masses have obvious brittleness and anisotropies under uniaxial stress, and the anisotropies are largely influenced by the geometric distribution of joints. Under confining pressures, the mechanical properties of rock masses have obvious ductileness, and the anisotropies of rock masses decrease and tend to the isotropies with the confining pressure. (2) The initial axial strain of conventional triaxial compression can not be ignored in higher confining pressure if the compaction of rock masses is considered.