• Developing a combined KDC-GFDM scheme for long-time dynamic simulations. • Proposing a domain-decomposition GFDM for 3D anisotropic composite materials. • Introducing a new distance criterion for the adaptive selection of nodes in the GFDM. • Extremely large time step-sizes can be used in temporal discretization . In this paper we investigate the application of the generalized finite difference method (GFDM) to three-dimensional (3D) transient heat conduction in anisotropic composite (layered) materials. In our computations, the Krylov deferred correction (KDC) method, a pseudo-spectral type time-marching technique, is introduced to perform temporal discretization in time-domain. The KDC method allows discretizing the temporal direction using relatively large time-steps, making the method very promising for dynamic simulations, particularly when high precision is desired. A multi-domain GFDM scheme is also employed where the composite material considered is decomposed into several sub-domains and, in each sub-domain, the solution is approximated by using the GFDM expansion. On the sub-domain interface, compatibility of temperatures and normal heat fluxes is imposed. The method is tested on several benchmark numerical examples and its relative merits and disadvantages are discussed.