When hydrogen atoms occupy interstitial sites in metal lattices, they form metal hydrides (MHx), whose structural and electronic properties can differ significantly from those of the host metals. Determining where the hydrogen is located within the MHx is crucial for predicting and understanding the resultant unique physical and electronic properties of the hydride. Yet, directly imaging hydrogen within a host material remains a major challenge due to its weak signal in conventional X-ray and electron imaging techniques. Here, we employ electron ptychography, a scanning transmission electron microscopy (STEM) technique, to image the three-dimensional (3D) distribution of H atoms in palladium hydride (PdHx) nanocubes, one of the most studied and industrially relevant MHx materials. We observe an unexpected one-dimensional superlattice ordering of hydrogen within the PdHx nanocubes and 3D hydrogen clustering in localized regions within the PdHx nanocubes, revealing spatial heterogeneity in metal hydride nanoparticles previously inaccessible by other methods.