Fault zones, prevalent in deep geological strata, are commonly filled with fault gouge, rock debris and other fillings, significantly impacting the stability of rock masses. The shear mechanical properties of filled joints within fault fractures are intricate and influenced by various factors, including rock type and its mechanical properties, joint roughness, the mineral composition and mechanical characteristics of the fillings, and as well as interactions, such as groundwater. This paper reviews the research trajectory of the shear mechanical behavior of filled rock joints and provides a systematic summary of the current research status on their shear mechanical properties. The key issues and research progress of shear mechanical properties of filled rock joints are analyzed from the aspects of laboratory shear experiment, numerical simulation, shear strength criterion and constitutive model theory. The existing problems and development trends of different research methods were also analyzed. Presently, filling degree, mineral composition and mechanical properties of fillings are recognized as the most critical distinctions from unfilled rock joints. Additionally, factors like fluid interactions, normal stress, and joint roughness significantly affect the mechanical properties of filled joints. However, the shear strength theories developed through macroscopic phenomenological approaches struggle to find precise application in engineering practices. Future research will primarily tackle the shear mechanical properties of multi-scale rock joints with fillings, focusing on the meso-mechanisms of shear failure within filled joints, the development of shear criteria for different types of filled joints, and the corresponding numerical simulation models and mesoscopic parameter determinations. Investigating the complex behavior of multi-scale filled joints under multi-field coupling conditions is poised to become a leading and pressing research area.