The paper presents the experimental, numerical, and theoretical investigation of the microstructure of nickel aluminide samples manufactured by spark plasma sintering using electron backscatter diffraction and computer assisted software. The aim of the work was to reveal the evolution of the microscopic and macroscopic parameters related to the microstructure of the material and its dependence on the applied sintering parameters—temperature and pressure. The studied porous samples with different relative density were extracted from various planes and then tested by electron backscatter diffraction to evaluate the crystallographic orientation in every spot of the investigated area. On this foundation, the grain structure of the samples was determined and carefully described in terms of the grain size, shape and boundary contact features. Several parameters reflecting the grain morphology were introduced. The application of the electric current resulting in high temperature and the additional external loading leads to the significant changes in the structure of the porous sample, such as the occurrence of lattice reorientation resulting in grain growth, increase in the grain neighbours, or the evolution of grain ellipticity, circularity, grain boundary length, and fraction. Furthermore, the numerical simulation of heat conduction via a finite element framework was performed in order to analyse the connectivity of the structures. The numerical results related to the thermal properties at the micro- and macroscopic scale—local heat fluxes, deviation angles, and effective thermal conductivity—were evaluated and studied in the context of the microstructural porosity. Finally, the effective thermal conductivity of two-dimensional EBSD maps was compared with those obtained from finite element simulations of three-dimensional micro-CT structures. The relationship between the 2D and 3D results was derived by using the analytical Landauer model.