Given the long history of small-holder recycling, the irrigation of farmland and green spaces with rural domestic sewage is increasingly drawing attention for its water and nutrient reuse potential. However, the long-term effects of using treated rural domestic sewage for irrigation in farmland and green spaces within semi-arid regions are rarely reported. Here, a 2-year field investigation was conducted to assess the influence of sewage irrigation on microbial community and soil health. The study included two irrigation types of well water and treated rural domestic sewage across four village sites. Compared to well water, treated rural domestic sewage contains more mineral nutrients and organic matter, such as 7.74-46.25 mg/L of total nitrogen, 2.20-20.6 mg/L of ammonia nitrogen, 0.66-1.42 mg/L of total phosphorus, and 23.00-63.86 mg/L of chemical oxygen demand. The fungal Shannon index, bacterial metabolic functions (including xenobiotic biodegradation and metabolism), fungal pathotroph-saprotroph functional taxa, and bacterial and fungal network complexity were all reduced in soil irrigated with treated rural domestic sewage. Meanwhile, the relative abundances of Pseudomonas, Polaromonas, Aromatoleum, and Legionella among bacteria, as well as Fusicolla, Beauveria, and Emericellopsis within fungi, were observed to increase in soil irrigated with treated rural domestic sewage. This enrichment led to an improvement in the symbiotrophic functional taxa of fungi, microbial network complexity, and the soil health index in poor health conditions. This could be explained by the increased availability of specific nutrients when irrigating with treated rural domestic sewage, which may recruit some beneficial microorganisms in the soil. Mantel test and path model revealed that soil nitrogen and phosphorus influenced the soil health index by driving the structure and complexity of bacterial and fungal communities and their associated networks. Phosphorus exhibited an extremely significant correlation with the bacterial community, enhancing the soil health index by increasing the complexity of the bacterial network, which counterbalanced the negative effect of irrigation with treated rural domestic sewage on soil microbiome. In conclusion, this study not only highlighted the efficacy of irrigation with treated rural domestic sewage in improving poor soil health conditions but also illustrated potential microbial mechanism by influencing community structure and network dynamics. This suggests that treated rural domestic sewage could be used as an irrigation source in semi-arid area.