This paper demonstrates hydrogen ion (H+) induced structural and mechanical changes in Zircaloy-4 correlated with its surface morphology. The specimens of Zircaloy-4 were irradiated with H+ at room temperature using a pelletron accelerator. The ion energy was varied from 1 to 4 MeV in four equal steps while keeping the dose fixed at 1 × 1014 H+ cm−2. The range of H+ inside Zircaloy-4, investigated through SRIM software, was 10.4 μm, 29.1 μm, 54.1 μm and 85 μm for 1 MeV, 2 MeV, 3 MeV and 4 MeV irradiated specimens, respectively. X-ray diffraction patterns of irradiated Zircaloy-4 exhibited variations in the width and position of Zr diffraction peaks. The Williamson–Hall analysis of these peaks depicted inconsistent changes in crystallite size and strain with increase of H+ energy. The surface morphology revealed the formation of bubbles and cavities in specimens irradiated with 1 MeV ions. With increasing ion energy above 1 MeV, small cavities and particles clusters were observed. The mechanical testing results indicated an increase in the micro-hardness of the sample irradiated with 1 MeV H+, however, the micro-hardness decreased with increase of ion energy greater than 1 MeV. The obtained results were elucidated on the basis of variable energy H+ interaction with Zircaloy-4 and annihilation of ions induced defects at higher energies.