We present morphological and compositional analysis of phase-separated Pt-Ni alloy nanoparticles (NPs) formed by ns pulsed laser dewetting. The PtNi NPs obtained by the pulsed laser dewetting consist of phase-separated multiple domains including Pt3Ni, PtNi and PtNi3 phases with various crystal orientations as revealed by transmission electron microscopy, which is in contrast to thermal dewetting resulting NPs of a uniform composition. A three-dimensional (3D) electron density map of a dewetted PtNi NP obtained using the coherent x-ray diffraction microscopy elucidates the 3D morphology of Pt- and Ni-rich regions together with a nano-cavity formed during the pulsed laser irradiation.