Arachnids constitute the primary predatory arthropod taxa in desert ecosystems, and as predators, they play a crucial role in maintaining and facilitating the coexistence of arthropod diversity within these ecosystems. In light of this, this study utilises dynamic monitoring data from 72 uniform 8 m × 8 m grids in the Gobi Desert spanning from 2012 to 2020. The aims are to analyse the spatiotemporal patterns of composition and diversity in arachnid arthropod communities, and to ascertain the impact and regulatory mechanisms of precipitation, temperature, and shrub interactions on arachnid arthropod assemblage. The key findings are as follows: (1) Karschiidae, Phalangiidae, and Gnaphosidae constitute the main arachnid family in the Gobi Desert, with accounting for 17.78%, 27.29%, and 27.35%. (2) There is significant annual variation in the composition of the arachnid community, and increases in precipitation boost the population of Karschiidae and Phalangiidae, thereby enhancing the abundance and diversity of arachnids. (3) The spatial autocorrelation distance between arachnids and major families varies seasonally and annually, with significant positive correlations observed between arachnid communities and the abundance of dominant families captured within the ranges of 9.0–30.0 m and 5.1–48.9 m. (4) There is a significant positive correlation between annual precipitation and the activity density of Karschiidae, Gnaphosidae, and Lycosidae; in contrast, the annual average temperature is only significantly positively correlated with the activity density of Gnaphosidae. The coverage of Nitraria sphaerocarpa demonstrates a stable positive correlation with the number of individuals in the arachnid community during wet years (2012–2015, 2020), whereas the influence of Reaumuria songarica exhibits interannual specificity, showing a significant positive correlation only in 2013 and 2016. In summary, changes in climate, vegetation, shrubs, and soil environment strongly affect the spatiotemporal distribution pattern of arachnids in the Gobi Desert.