The batch mode of vacuum membrane distillation–crystallization (VMDC) process was carried out in the ammonium salt solutions. Vacuum membrane distillation (VMD) was used to permeate water to a desired concentration and the crystallizer was applied for the precipitation of crystals. The influence of concentration time on the permeate flux was investigated and the transfer resistances were estimated. Membrane fouling resistance increased gradually when the solution was concentrated up to the critical point of supersaturation factor. Beyond this critical point, the NH4Cl system revealed an irreversible membrane fouling, whereas the (NH4)2SO4 system revealed a reversible membrane fouling. By analyzing the transfer resistances, the determining concentration in the VMD process could be obtained, which would provide a way of avoiding membrane fouling problem. The permeated total nitrogen (TN) increased significantly from 4.7 to 59.8 mg/L with the NH4Cl solution. However, low level permeated TN (TN < 3 mg/L) with (NH4)2SO4 solution was maintained during the whole concentration process. The NH4Cl crystals with dendritic structure and (NH4)2SO4 crystals of lamellar form were obtained by the crystallizer with the production of 125.7 and 58.4 kg/m3, respectively.