Computational models simulating the crystallisation of hexagonal close packed (hcp) metals have traditionally used simple solid/fluid interface anisotropy relations. However, this method does not provide a proper representation of the crystallisation anisotropy, particularly for non-isothermal crystallisation. In this work, we used a phase field (PF) model to investigate the effects of thermal properties (thermal diffusivity and latent heat) on the morphological evolution of hcp metals during crystallisation. The governing equation of the PF model was coupled to the temperature evolution equation, and a three-dimensional model was developed in a finite element framework using COMSOL software. We applied the model to study the crystal formation and evolution of magnesium and yttrium. The unique aspect of this work is that we used Qin and Bhadeshia's three-dimensional interface anisotropic model to accurately simulate solid/fluid interface anisotropy. The results showed that the thermal effects significantly influenced the shape evolution of the crystals and can control the formation of potential sites for void nucleation inside the crystal structures.