This work extends the previous two-dimensional compact scheme for the Cahn-Hilliard equation (Lee et al., 2014) to three-dimensional space. The proposed scheme, derived by combining a compact formula and a linearly stabilized splitting scheme, has second-order accuracy in time and fourth-order accuracy in space. The discrete system is conservative and practically stable. We also implement the compact scheme in a three-dimensional adaptive mesh refinement framework. The resulting system of discrete equations is solved by using a multigrid. We demonstrate the performance of our proposed algorithm by several numerical experiments. (C) 2015 Elsevier B.V. All rights reserved.