Rainfall is considered as the dominant water replenishment in desert ecosystems, and the conversion of rainfall into soil water availability plays a central role in sustaining the ecosystem function. In this study, the role of biological soil crusts (BSCs), typically formed in the revegetated desert ecosystem in the Tengger Desert of China, in converting rainfall into soil water, especially for the underlying soil moisture dynamics, was clarified by taking into account the synthetic effects of BSCs, rainfall characteristics, and antecedent soil water content on natural rainfall conditions at point scale. Our results showed that BSCs retard the infiltration process due to its higher water holding capacity during the initial stage of infiltration, such negative effect could be offset by the initial wet condition of BSCs. The influence of BSCs on infiltration amount was dependent on rainfall regime and soil depth. BSCs promoted a higher infiltration through the way of prolonged water containing duration in the ground surface and exhibited a lower infiltration at deep soil layer, which were much more obvious under small and medium rainfall events for the BSCs area compared with the sand area. Generally, the higher infiltration at top soil layer only increased soil moisture at 0.03 m depth; in consequence, there was no water recharge for the deep soil, and thus, BSCs had a negative effect on soil water effectiveness, which may be a potential challenge for the sustainability of the local deep‐rooted vegetation under the site specific rainfall conditions in northwestern China.