Aeration drip irrigation (ADI) promotes crop growth and productivity, possibly by changing soil microorganisms. However, the impact of ADI on soil microbial communities, especially changes in the archaea community, remain unclear. We conducted a three-season tomato field experiment in Shouguang, China, to investigate changes in soil archaeal communities under three dissolved oxygen concentrations (10, 15, and 20 mg·L^–1) compared to a control (CK) treatment (no aeration). ADI increased α-diversity values and changed the dominant phyla and genera of archaea. In addition, the ADI treatments had more intra-kingdom linkages and higher edge and average clustering coefficients than the CK treatment, resulting in a more complex archaeal network. The soil C/N (organic carbon/total nitrogen) ratio and nitrate-nitrogen (NO₃^–-N) predominantly drove the key species changes in the archaeal network. The key species (e.g., Micrarchaeota, Thermoplasmatota, and Thaumarchaeota) were significantly associated with functional genes related to C and N cycles. More importantly, archaea contributed more to microbial resistance than bacterial and fungal resistance, but they were not at the network's core. The structural equation model revealed that high microbial resistance, directly or indirectly, improved tomato yields by regulating soil dissolved organic carbon (DOC) and NO₃⁻-N contents. This study offers the first integrated insights into soil archaeal communities, ecological resistance index, soil nutrients, and tomato yield under ADI, which will guide future efficient agricultural production.