Deep underground rocks exhibit significant layered heterogeneity due to geological evolution and sedimentation. Rock fracture toughness, as one of the important indicators of hydraulic crack propagation, also exhibits heterogeneous distribution. In order to investigate the influence of non-uniform fracture toughness of layered rocks on hydraulic crack propagation, this paper establishes a planar three-dimensional hydraulic crack propagation model. The model is numerically solved using the 3D displacement discontinuity method (3D-DDM) and the finite difference method. The calculation results indicate that when the distribution of the fracture toughness of layered rocks changes from uniform to non-uniform, the fracture morphology develops from a standard circular crack to an elliptical crack. When the difference of the rock fracture toughness between adjacent rock layers and the middle rock layer (pay zone) is large enough, the fracture morphology will develop towards a rectangular shape. In addition, when the fracture toughness of rock layers is non-uniformly distributed, the hydraulic crack not only rapidly expand in the softening layer (rock layer with lower fracture toughness), but also slowly propagate in the strong layer (rock layer with higher fracture toughness). However, the propagation speed in the softening layer is much faster than that in the strong layer. The results indicate that the heterogeneity of rock fracture toughness has an important impact on the morphology, propagation speed, and direction of hydraulic fractures.