It is known that changes on the microscopic, structural level of materials exert changes on their macroscopic properties, in particular elastic ones. This approach can be used to alter the elastic properties of materials. However, it is not easy to predict the impact of a particular change in the structure of crystals. The recent studies show that depending on the size, shape, and orientation of inclusions used, the resulting elastic properties may differ. Inclusions may enhance, weaken, or eliminate the auxetic properties in a hard sphere model. This study is focused on the influence of the spatial distribution of planar inclusions within the hard sphere crystal and its impact on its elastic properties. Periodic systems containing two nanolayer inclusions in the representative volume element, oriented orthogonally to ‐direction and in various spatial ordering, are considered. It has been shown that introducing layer inclusions causes the deterioration of auxetic properties in the ‐direction. However, the latter weakly depends on the spatial ordering of the inclusion layers. Moreover, changes in the size of the inclusion particles, combined with different ordering of the inclusion layers, can be used to coarsely and finely tune the elastic properties of the model crystal.