Abstract Root-pathogen interactions are an important factor accelerating premature senescence of rice, however, few study have addressed the underlying interactions in rhizosphere micro-ecosystem. In this study, the OsVHA-A1 mutant rice line displayed an early senescent phenotype associated with a special rhizosphere microbiome in contrast to the wild type. Moreover, the pathogen Gibberella intermedia had been shown to sharply increase when premature senescence occured in OsVHA-A1 mutant. Using GC-MS analysis, we found the composition of root exudates from the senescent rice were different from the WT. In addition, transcriptome data revealed that G. intermedia preferred using sugars from root exudates that had been generated by fructose and mannose metabolism in the mutant. Furthermore, the OsVHA-A1 mutant would display cell death in both physiological and molecular levels when suffering from pathogenic infection by G. intermedia. However, such fungi showed a weaker virulence for infecting the WT. Finally, Bacillus and Burkholderia could be used as antagonistic bacteria that could effectively alleviate the early senescent phenotype of OsVHA-A1 mutant rice thereby improved its grain yield. Keywords: OsVHA-A1, premature senescence, microbiome, G. intermedia, GC-MS, transcriptome, sugars, virulence, cell death, antagonistic bacteria