Background and aimsFrequent extreme weather poses significant threats to agricultural production and biological communities. Understanding the microbiological mechanisms that determine plant health under warming fluctuations (including short-term warming (WM, 45 degrees C for lasting 10 days) and recovery from warming (RE, the end of warming and returning to 25 degrees C for lasting 10 days)) is crucial for achieving sustainable agricultural development.MethodsHere, we explored the effects of warming fluctuations on the plant health index (PHI) and on the bacterial and fungal communities in both bulk soil and rhizosphere.ResultsWarming fluctuations did not change the rhizosphere bacterial or fungal alpha diversity but did affect the community structure and composition in both the bulk soil and rhizosphere. Moreover, warming fluctuations altered the stability and complexity of the bacterial and fungal networks, and the changes exhibited obvious differences between the bulk soil and rhizosphere. Bacterial and bulk soil fungal taxa enhanced their cooperation to adapt to WM, while rhizosphere fungal taxa became more competitive. In addition, warming fluctuations reduced the wheat health index and caused irreversible damage. Biotic factors, particularly core taxa such as Nocardioidaceae, Trueperaceae, Microbacteriaceae, and 67-14 of bacteria, as well as Diversisporaceae, Glomeraceae, Entolomataceae, and Orbiliales of fungi, have emerged as the main driving forces affecting wheat health. These core taxa can directly influence wheat health or indirectly regulate network complexity and competition among taxa.ConclusionsOur study underscores the significance of core taxa in modulating soil microbiome dynamics and safeguarding plant health, offering valuable insights and strategies for enhancing crop productivity and fostering sustainable agricultural development amidst increasingly frequent extreme weather events.