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Water availability is a major limiting factor in desert ecosystems. However, a winter snowfall role in the growth of biological soil crusts is still less investigated. Here, four snow treatments were designed to evaluate the effects of snow depth on photosynthesis and physiological characteristics of biological soil crusts. Results showed that snow strongly affected the chlorophyll fluorescence properties. The increased snow depth led to increased contents of photosynthetic pigments and soluble proteins. However, all biological soil crusts also exhibited a decline in malondialdehyde and soluble sugar contents as snow increased. Results demonstrated that different biological soil crusts exhibited different responses to snow depth treatment due to differences in their morphological characteristics and microhabitat. In addition, interspecies differentiation in response to snow depth treatment might affect the survival of some biological soil crusts. Further, this influence might lead to changes in the structural composition and functional communities of biological soil crusts.