Water is the most important limiting factor for plant growth in desert. Biological soil crusts (BSCs), as important community soil-surface organisms in desert, tend to occupy interspaces between vascular plants in arid ecosystems and play an important role in soil hydrological processes, especially water evaporation and infiltration. Previous studies showed that the uncertain change of precipitation patterns has led to the mortality of the desert moss crusts. However, it is not clear whether moss mortality affects the evaporation and infiltration of the crusted topsoil water. In this study, moss crusts dominated by Syntrichia caninervis were selected to investigate the effects of moss mortality on soil water evaporation and infiltration in Gurbantunggut desert. Three different surface types were included in this paper, there were living moss crust, dead moss crust and bare sand (as control). Soil water evaporation and infiltration were measured by using Mini-Disk Infiltrometer and Evaporation meter. In order to provide a theoretical basis for further study of the impact of desert moss crusts on the hydrological processes of desert ecosystem. The results showed that moss crusts significantly inhibited water infiltration compared with bare sand, and the inhibition degree of dead moss crusts was the greatest. The initial infiltration rate, steady infiltration rate and cumulative infiltration amount of dead moss crusts were 39.89%, 85.91% and 64.48% of those of living moss crusts, and were 5.96%, 13.13% and 20.42% of bare sand, respectively. In the initial stage of water evaporation, the evaporation rate of bare sand was significantly higher than that of living moss and dead moss crusts, but the time for maintaining a relatively stable evaporation rate of dead moss crusts was longer than that of bare sand and living moss crusts, which also led to the highest final cumulative evaporation of dead moss crust and the lowest of bare sand. Our results indicated that moss mortality of moss-dominated BSCs could significantly reduce soil water infiltration and increase water evaporation, which would consequently affect the soil water distribution pattern and thus affect the relationship between BSCs and vascular plants water use. This study demonstrates the important effects of biological soil crusts upon soil hydrological processes. At present, it is an indisputable fact that global warming has led to the extinction of a large number of species. Therefore, it is of great importance to evaluating the ecological effects of mosses mortality in arid and semi-arid environments. The results of this paper not only can provide certain scientific basis for revealing the response mechanism of the hydrological processes of BSCs to global warming, but also can provide a theoretical basis for protecting the species diversity of desert plants and surface stability in desert.