In periodic W/Be multilayers, thickness-dependent microstructural and phase modifications were investigated in W and Be layers. In X-ray diffraction, α-W was predominant for the ultrathin layer of W, while β-W evolved along with the α-W phase for higher film thickness. For the thicker layers, the thermodynamically metastable β-W vanished and a single well-defined preferably oriented stable α-W phase was observed. The lattice spacing revealed that these phases exist in the tensile stressed condition. With the increase in thickness of Be layers, the blueshift and narrow linewidth of the transverse optical (TO) phonon mode was observed in Raman scattering studies. However, the TO mode was redshifted and the linewidth was further narrowed consistently with an increase in the thermal annealing temperature of the multilayers. The investigation has quantified an increase in compressive strain and reduction of defects with an increase in thickness of the Be layers. However, for thermally annealed samples, the compressive strain in the Be layers was relaxed and crystalline quality was improved.