Research on the equivalent deformation parameters of grouted arch dam abutment rock masses has recently emerged as a key in the design, construction and stability assessment of arch dams. With the aim of synthetically considering scale effects and anisotropy of the rock mass equivalent deformation parameters after grouting, in this paper, a practical numerical calculation method is developed. First, the Latin hypercube sampling method is introduced to generate a network of fractures of the arch dam abutment rock mass. Subsequently, the finite element models of the rock masses with different sizes in various directions are constructed. On this basis, equivalent continuum theory and cohesive element model are applied for numerical calculation of grouting fractured rock masses. Then, the scale effect and anisotropy of the deformation modulus of rock mass under different grouting conditions are investigated. Finally, the Jinping super-high arch dam is taken as an example to validate the theoretical significance and application effect of the proposed method. The analysis results indicate that the process of fracture and fragmentation of grouted rock masses is characterized precisely, and the deformation of material units can be described as fully as possible to calculate more realistic equivalent deformation parameters of the fractured rock masses.