Electron beam (e-beam) irradiation effects on ZnO single crystals have been investigated by using time-of-flight electron-stimulated desorption (TOF-ESD). The samples were irradiated by using a continuous 0.5 or 1.5 keV e-beam, while the TOF-ESD spectra were taken by using a pulsed 0.5 keV e-beam. For both the O-terminated and Zn-terminated surfaces, the major desorption is H+ desorption. The main trend of H+ desorption intensity and evolution as a function of irradiation time is similar for both faces. The H+ peak is much higher after 1.5 keV irradiation than after 0.5 keV irradiation. The intensity of the H+ peak decreases exponentially as a function of irradiation time and partially recovers after the irradiation is stopped. These observations suggest that the main contribution of the H+ desorption is hydrogen released from the dissociation of H-related defects and complexes in the bulk region of the ZnO by e-beam irradiation. This finding can be used to explain the reported ultraviolet degradation of ZnO single crystals under electron irradiation observed by cathodoluminescence. The surfaces play a lesser role for the H+ desorption, as there are differences of the decreasing rate between the two faces and additionally the intensity of the H+ peak for both the unclean O-face and Zn-facesis smaller than that for clean faces. While the H+ desorption is mainly dominated by the bulk region, O+ desorption is more influenced by the surfaces. There are two kinds of O+ desorbed from ZnO having 13.0 μs TOF and 14.2 μs TOF. The O+ desorption depends on the surface polarity, the surface conditions and the energy used for irradiation.