In drylands, microalgae dwelling in the biocrust are inevitably confronted with nitrogen deficiency and desiccation stress, despite the protection afforded by the soil biological complex. However, the environmental adaptive features and mechanisms of these microalgae remain largely unknown. In this study, we explored the adaptive changes of a biocrust-derived unicellular microalga, Vischeria sp. WL1 (Eustigmatophyceae), in the face of long-term nitrogen deficiency. Attention was focused on the alterations in cell wall properties and the associated desiccation resistance. After exposure to long-term nitrogen deficiency, the cell walls of Vischeria sp. WL1 thickened substantially, accompanied by enhanced rigidity and an improvement in desiccation resistance. In contrast, Vischeria sp. WL1 cells cultivated under nitrogen-replete conditions were highly vulnerable to desiccation stress. Additional cell wall alterations after nitrogen starvation included distinct surface sculpturing, variations in monosaccharide composition, and changes in functional groups. Collectively, this study provides valuable insights into the survival strategies of biocrust-derived microalgae in nitrogen-deficient dryland environments.