The phase‐field crystal model allows the study of materials on atomic length and diffusive time scales. It accounts for elastic and plastic deformation in crystal lattices, including several processes such as growth, dislocation dynamics, and microstructure evolution. The amplitude expansion of the phase‐field crystal model (APFC) describes the atomic density by a small set of Fourier modes with slowly‐varying amplitudes characterizing lattice deformations. This approach allows for tackling large, three‐dimensional systems. However, it has been used mostly for modeling basic lattice symmetries. In this work, we present a coarse‐grained description of the hexagonal closed‐packed (HCP) lattice that supports lattice deformation and defects. It builds on recent developments of the APFC model and introduces specific modeling aspects for this crystal structure. After illustrating the general modeling framework, we show that the proposed approach allows for simulating relatively large three‐dimensional HCP systems hosting complex defect networks.