Biological soil crusts (biocrusts) are widely distributed in global drylands. Both the succession of biocrusts and increased precipitation levels have the capacity to augment soil water availability, thereby exerting significant influence on soil eukaryotic communities. Nonetheless, our understanding of the combined effects of biocrust succession and increasing precipitation on soil eukaryotic communities remains less comprehensive when compared to the well-documented impacts on soil prokaryotic and archaeal communities. In this study, we conducted a broad survey in Chinese deserts and collected biocrust samples in a transect with increasing precipitation. We obtained soil eukaryotic community data using high-throughput sequencing. Our statistical analyses revealed the following key findings: (1) In the absence of biocrusts (within bare soil), there existed a negative correlation between precipitation levels and eukaryotic diversity, as well as community similarity; however, within any of the biocrust successional stage, these patterns turned to be V-shaped, initially declined and then increased, with the nadir occurring at intermediate precipitation levels. (2) Biocrust succession markedly enhanced the abundances of mosses, and which were particularly higher under moderate than other precipitation levels. (3) The abundance of mosses emerged as the principal driver of soil eukaryotic community dynamics, wherein higher moss abundance correlated with diminished species diversity but complex species co-occurrence networks in late biocrust successional (the lichen and moss) stages and under moderate precipitation levels. (4) Soil C:P emerged as a pivotal factor mediating moss abundance and influencing the patterns observed in soil eukaryotic communities. In summary, our study concludes that biocrust succession alters the variation patterns of soil eukaryotic communities along the precipitation gradient.