Rock joints in fault zones are commonly filled with fault gouge, where clay fillings are common. Until now, the shear characteristics of filled rock joints under different moisture contents and shear rates have not been well understood. This work investigates the mechanical behaviour of rock-like materials with clay-filled joints under compression-shear loading. A self-developed rock shear test system was used to conduct direct shear tests on rock-like materials under three normal stresses and five shear rates. Six types of natural red clay with different moisture contents were selected for filling. The coupling effects of the moisture content and shear rate on the mechanical properties of rock-like samples with clay-filled joints were investigated. Furthermore, the failure characteristics of the failure surfaces of rock-like materials after shearing were scanned via 3D scanning. The test results show that the moisture content of fillings and shear rate significantly affect the shear characteristics of rock-like materials with filled joints. The plastic limit moisture content is a critical point where the shear rate has the least effect on the shear strength. Under dry soil filling conditions, the degree of shear damage on the shear plane is the smallest. The present results can provide guidance for slope protection projects.