Paenibacillus polymyxa is a promising biocontrol agent based on many applications in agriculture. In this study, characterization of a novel strain JX-1 was performed by various comparative phenotypic assays including cell wall-degrading enzyme activity assay, antagonism in vitro and in planta and multi-omics analysis consisting of whole-genome sequencing and metabolomic analysis. The results showed that JX-1 produced protease, cellulase, and pectinase, with protease activity exceeding other P. polymyxa strains. The supernatant and VOCs produced by JX-1 both contain components that effectively antagonize both bacteria and fungi. JX-1 inhibited Fusarium verticillioides, Sclerotinia sclerotiorum, Botrytis cinerea and Sclerotium rolfsii. Furthermore, it significantly reduced the severity of clubroot in Arabidopsis thaliana and Brassica rapa in planta, resulting in an improvement in the total shoot fresh weight. The closely related P. polymyxa strain JX-2 (ANI = 99.96% compared to strain JX-1) was used for comparative phenotyping and multi-omics analysis that implicated extracellular proteases and some small peptides could be essential for clubroot biocontrol. Genomic analysis of strain JX-1 confirmed that it is indeed P. polymyxa (ANI > 95% compared to reference strains). Moreover, JX-1 harbors predicted carbohydrate-active enzymes (CAZymes), 16 extracellular protease genes, and 17 gene clusters with biosynthetic potential (NRPS/PKS hybrids). Metabolomic profiling of the culture supernatant further identified differential accumulation of hydrophobic-amino-acid-containing small peptides, providing a metabolic basis for the observed antagonism and offering leads for future mechanistic studies. These findings establish JX-1 as a broad-spectrum biocontrol agent against clubroot disease.