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Despite extensive studies on the taxonomic diversity and metabolic capacity of microbiomes in response to drought, drought effects on the soil microbial co-occurrence networks and their function roles are less understood. This is partly due to the distinct microbial composition and activities in the rhizosphere compared to bulk soil.Here, we conducted a 2-year controlled watering experiment to examine the effects of drought on the network structure and functions of soil microbiomes in both the rhizosphere and bulk soil of the native grass <i>Bothriochloa ischaemum</i>. We evaluated the secretion rate and composition of root exudates linked to microbial variation under three different watering regimes: well-watered (80% field capacity), moderate drought (60% field capacity), and severe drought (40% field capacity). Microbial community composition was analyzed using amplicon sequencing, and functional gene abundance was quantified via qPCR.We found that, compared to the weak response of the microbial community in the bulk soil, drought markedly reduced the diversity of bacteria, fungi and protists, their network complexity (e.g., nodes and edges numbers, average degree, modularity, and clustering coefficient), and the abundance of genes related to C degradation (<i>sga</i>,<i> amyX</i>,<i> abfA</i>,<i> and xlyA</i>), N fixation (<i>nifH</i>), ammonification (<i>ureC</i>), denitrification (<i>nirK</i> and <i>nirS</i>), and assimilatory (<i>nasA</i>) and dissimilatory (<i>napA</i>) N reduction in the rhizosphere. The reduction in microbial network complexity and reduced C- and N transformation genes were highly correlated with the drought-induced decline in root C exudation and changes in the component diversity of exudate components, including amino acids, lipids, organic acids, vitamins, cofactors and carbohydrates. Among the root exudates, organic acids played a crucial role in shaping microbial occurrence networks, while amino acids were essential in regulating functional genes involved in C and N cycling.