Biological-soil crusts, a community of cyanobacteria, lichens, and mosses that live on the soil surface, are a critical part of land cover types in desert ecosystems. They play a significant role in many biogeochemical processes, contributing to soil fertility, stability, and vascular plant establishment. The photosynthetic and respirometric activity of biological-soil crusts can affect carbon fluxes and exchange in desert ecosystems. Water is the major limiting factor of ecosystem functions and processes in arid and semi-arid regions. In environments with dry climates, scarce precipitation, and water shortages, water can affect the photosynthesis and respiration of biological-soil crusts, leading to changes in carbon fluxes and exchange in the soil. In the present study, to determine the effect of biological-soil crusts on soil carbon fluxes under different amounts of precipitation, we used the two dominant soil crusts types found in the Qinghai-Tibet Plateau alpine sandy vegetated areas: moss and algae. Five different simulated precipitation amounts (1, 2, 5, 10, and 0 mm) were applied, and the carbon flux of soil covered by biological crusts was measured using Li-8100 in the dark as dark respiration and in the light as the net carbon flux. The results show that the: (1) net carbon flux and dark respiration of biological-soil crusted soil were stimulated by simulated precipitation, and increased rapidly to their maximum levels. There was a significant difference between the precipitation treatments and control, but no significant difference between different treatments. The maximum carbon flux and stimulated available time of moss-crusted soil were much higher and longer, respectively, than those of algae-crusted soil; (2) total accumulated carbon release of two crusted soils after the addition of simulated precipitation increased with increasing precipitation, and there was a significant difference between carbon release in the precipitation treatments and the control. The total accumulated carbon release of moss-crusted soil was significantly more than that of algae-crusted soil; (3) carbon flux of two crusted soils and the soil volumetric water content showed a significant correlation. The effects of soil water on net carbon flux and dark respiration were stimulative. The results of the analysis indicated that the biological-crusted soil showed an effect of the carbon source after the addition of simulated precipitation. Precipitation can directly influence the carbon flux and release, and the response of the carbon flux in biological-soil crusted soil to simulated precipitation should be considered when studying carbon exchange in arid and semi-arid regions.