【Objective】Intensive monoculture practices can degrade land, but the specific impacts of long-term, high-intensity citrus cultivation on soil microbial communities and soil multifunctionality are not well understood.【Method】This study examined soils from citrus orchards of varying planting durations, using high-throughput sequencing to assess the influence of intensive cultivation on soil microbial communities. It also investigated soil multifunctionality, microbial diversity, and co-occurrence networks associated with carbon, nitrogen, and phosphorus cycling. 【Results】This study indicated that soil bacterial diversity declined significantly as the duration of citrus cultivation increases. The Shannon index decreased from 7.05 in 5-year soils to 5.79 in 30-year soils, with species numbers dropping from 2 110 to 1 153. Microbial network complexity was also reduced in 30-year soils, with fewer taxa and fewer inter-taxa associations than in 5-year soils. Network nodes declined from 1 491 to 815, and edges from 8 449 to 2 369. Network complexity and stability varied significantly across citrus ages, with younger (5-year) soils showing greater complexity and stability than older (30-year) soils. Also, long-term citrus cultivation led to soil acidification, altering bacterial activity, community structure, and species composition. This included an increase in dominant taxa like Proteobacteria, Actinobacteria, and Firmicutes, and a decline in Acidobacteria, Chloroflexi, and Gemmatimonadetes. The relative abundance of nitrogen-cycling bacteria also increased, supporting processes such as nitrogen fixation, aerobic ammonia oxidation, denitrification, and aerobic nitrite oxidation. Changes in microbial diversity and structure correlated closely with shifts in soil multifunctionality, influenced by high-intensity citrus cultivation. The number of microbial network nodes showed a negative correlation with carbon cycle multifunctionality (CMF) and positive correlations with nitrogen cycle (NMF) and phosphorus cycle multifunctionality (PMF). The number of edges correlated negatively with CMF, positively with NMF, and was not significantly associated with PMF. 【Conclusion】Microbial diversity drives the complexity of microbial co-occurrence networks, significantly correlating with the number of network nodes and edges. Collectively, these findings indicate that prolonged citrus cultivation significantly reduces soil microbial diversity and impairs multiple ecological functions.