Zirconium tritiated (ZrT x ) is an alternative target material for deuteron-triton (D-T) reaction neutron generator. The isotopic replacement and microstructure evolution induced by hydrogen isotope implantation could significantly affect the performance of the target film. In this work, the zirconium deuteride film deposited on Mo/Si substrate was implanted by 150 keV protons with fluence from 1×10 16 to 1×10 18 protons/cm 2 . After implantation, the depth profiles of retained hydrogen (H) and deuterium (D) in these target films were analyzed by elastic recoil detection analysis (ERDA), and time of flight-secondary ion mass spectrometry (ToF-SIMS). Additionally, the microstructure evolution was also observed by x-ray diffraction (XRD) and scanning electron microscope (SEM). The D concentration in the ZrD x film decreased versus the proton implantation fluence. An analytical model was proposed to describe the hydrogen isotopic trapping and exchange as functions of incident protons fluence. Additionally, the XRD analysis revealed that no new phase was formed after proton implantation. Furthermore, circular flakings were observed on the ZrD x surface from SEM images at fluence up to 1×10 18 protons/cm 2 , and this surface morphology was considered to associate with the hydrogen atoms congregation in Mo/Si boundary.