To investigate the collision processes of proton with the water dimer (H2O)2 at 50 eV, the time-dependent density functional theory coupled with molecular dynamics nonadiabatically is applied. Six specific collision orientations with various impact parameters are considered. The reaction channels, the mass distribution and the fragmentation mass spectrum are explored. Among all launched samples, the probability of the channel of NCT and CT is about 80%, hinting that the probability of fragmentation is about 20%. The reaction channel of PE2 is taken as an example to exhibit the detailed microscopic dynamics of the collision process by inspecting the positions, the respective distance, the number of loss of electrons and the evolution of the electron density. The study of the mass distribution and the fragmentation mass spectrum shows that among all possible fragments, the fragment with mass 36 has the highest relative abundance of 65%. The relative abundances of fragments with mass 1, 35 and 34 are 20%, 13% and 1.5%, respectively. For the total electron capture cross section, good agreement has been achieved between the present calculations and the available measurements and calculations over the energy range of 50 eV to 12 keV.