• High amounts of non-rainfall water (10%–15% of water input) occur in the alpine sandy land. • Biological soil crusts increase the daily mean non-rainfall water amount by 23%–30%. • Biological soil crusts enhance non-rainfall water accumulation and dissipation rates by >20%. • The effects of soil crusts can be attributed to changes in soil physicochemical properties. • The principal source of non-rainfall water is atmospheric vapor (∼60%). Non-rainfall water originating from atmospheric and soil vapors is a major water source that supports dryland ecosystem functioning. The alpine sandy land ecosystem is fragile, where biological soil crusts develop widely on the soil surface and play a critical role in regulating surface hydrological processes. Yet, the effects of biological soil crusts on non-rainfall water in the alpine sandy land remain unclear. Therefore, we investigated the patterns and main sources of non-rainfall water under different biological soil crusts in the Qinghai–Tibet Plateau region during the growing season (May–September 2017). Micro-lysimeters were used to measure the amount of non-rainfall water in surface soil (0–10 cm) covered with moss and algae crusts in an interdune area. The results revealed that non-rainfall water occurred for at least 12 h·d −1 (7 p.m.–7 a.m.) and disappeared for 5 h (7 a.m.–12 a.m.). The daily mean non-rainfall water amount ranged between 0.324 and 0.426 mm. Differences in the physical and chemical properties of surface soil caused by biological soil crusts affected the accumulation and dissipation of non-rainfall water. The accumulation and dissipation rates of non-rainfall water under biological soil crusts were respectively 1.22–1.32-fold ( F = 8.01, P < 0.05) and 1.21–1.27-fold ( F = 8.86, P < 0.05) higher than those of bare sand. Biological soil crusts also increased the amount of total non-rainfall water by 23.41%–30.39% ( F = 5.367, P < 0.05), accounting for 2.4%–3.0% of the total water input. Atmospheric vapor condensation was the principal source of non-rainfall water (>60%). Nevertheless, biological soil crusts increased both atmospheric and soil vapor condensation by 29.44%–39.98% ( F = 12.45, P < 0.05) and 13.09–13.94% ( F = 5.91, P < 0.05), respectively. Although non-rainfall water contributed only 10%–15% of the total water input, it constituted a main water input to the ecosystem during the dry period of less rainfall (up to 20%, 19.72 vs. 95.72 mm). In conclusion, non-rainfall water, especially atmospheric vapor condensation, makes a non-negligible contribution to water input in the alpine sandy land ecosystem, for which biological soil crusts enhance the role of non-rainfall water in the water input in surface soil water balance dynamics.