In this paper, a third-order gas-kinetic scheme is developed on the three-dimensional hybrid unstructured meshes for the compressible inviscid and viscous flows. In the classical weighted essentially non-oscillatory (WENO) scheme, the high-order spatial accuracy is achieved by the non-linear combination of lower order polynomials. However, for the hybrid unstructured meshes, the procedures, including the selection of candidate stencils and calculation of linear weights, become extremely complicated, especially for three-dimensional problems. To overcome the drawbacks, a third-order WENO reconstruction is developed on the hybrid unstructured meshes, including tetrahedron, pyramid, prism and hexahedron. A general strategy is given for the selection of big stencil and sub-stencils for hybrid meshes, and the topologically independent linear weights are used in the spatial reconstruction. A unified interpolation is also used for the volume integral of different types of control volumes, as well as the flux integration over different cell interfaces. Incorporate with the two-stage fourth-order temporal discretization, the explicit high-order gas-kinetic schemes are developed for unsteady problems. With the lower–upper symmetric Gauss–Seidel (LU-SGS) methods and Jacobi iteration, the implicit high-order gas-kinetic schemes are developed for steady problems. To accelerate the computation, both explicit and implicit scheme is implemented with the graphics processing unit (GPU) using compute unified device architecture (CUDA). Especially, for implicit parallel computation, Jacobi iteration is used. The speedup of GPU code suggests the potential of high-order gas-kinetic schemes for the large scale computation. A variety of numerical examples, from the subsonic to supersonic flows, are presented to validate the accuracy and robustness for both inviscid and viscous flows.