Biological soil crust (BSC) is recognized as the ecosystem engineer, crucial in hastening the ecological restoration of degraded dryland environments and facilitating the carbon and nitrogen cycles. Mossy crusts, as a stable developmental stage in the succession of BSCs in arid and semi-arid regions, actively participate in the material cycle and energy flow of desert ecosystems. They also provide microhabitats supporting microbial diversity maintenance. Bacteria residing in these environments are integral to nearly all biogeochemical processes, potentially reshaping soil and ecosystem functionality and expediting ecosystem recovery. However, the intricate nature of microbial carbon and nitrogen metabolism poses challenges in understanding how the mossy crust microbiome influences biogeochemical cycling and the interconnected dynamics of the carbon and nitrogen cycles. In this study, we conducted metagenomic sequencing analysis about gene diversity related to carbon and nitrogen metabolism of microorganisms in soil which was attached to bryophyte (BRS) and soil which was dropped from bryophyte (BBS) in the Tengger Desert. Our aim was to gain a deeper insight into the contribution of microorganisms to the carbon and nitrogen cycle and the mechanism of carbon and nitrogen coupling in biological soil crusts. The results revealed that the dominant bacterial phyla with higher abundance were actively involved in carbon metabolism processes. Notably, the contribution of Chloroflexi to the carbon metabolic pathway in BBS was significantly greater than that in BRS (P < 0.001). Furthermore, we found a coupling effect between carbon and nitrogen metabolism in the microbiome of mossy crusts in the Tengger Desert. For instance, dissimilatory nitrate reduction showed a positive correlation with carbon metabolic pathways (P < 0.05). Denitrification was closely linked to the pentose phosphate pathway, 3-Hydroxypropionate bi-cycle, and lysine biosynthesis in the microbiome of mossy crusts (P < 0.05). BSCs influence the intricacy and resilience of bacterial networks within both the biocrust and subsoil layers of the Tengger Desert. Moreover, we found that the network connectivity of genes associated with carbon and nitrogen metabolism in the BRS microbiome exceeded that of the BBS, showcasing a more intricate web of gene interactions in BRS. Total phosphorus (TP) and total nitrogen (TN) were significant factors influencing the genes related to carbon and nitrogen processes in mossy crusts. The findings offer a metagenomic perspective on the role of soil microorganisms in nutrient accumulation and the coupling of carbon and nitrogen metabolism. This study also unveiled the intricate processes of carbon and nitrogen nutrient cycling as well as energy metabolism in mossy crusts in the Tengger Desert. It offers a foundational understanding of the molecular mechanisms through which microbes engage in carbon and nitrogen cycling.