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Seed‐borne pathogens can inhabit the rhizosphere and infect the plant after germination. The rhizosphere microbiome plays critical roles in defending against seed‐borne pathogens. However, the assembly of a core rhizosphere microbiome to suppress seed‐borne pathogens is unknown. Here, the root‐associated microbiome is infested with seed‐borne Fusarium in sterile environment, while the root‐associated microbiome is not infested when it interacts with the native soil microbiome across maize cultivars, suggesting that a core rhizosphere microbiome assembles to suppress seed‐borne Fusarium. Two strategies of progressive dilution and rhizodepositional attraction are applied to identify the core rhizobacteria. A synthetic microbiota (SynM) is constructed using the isolates of the core rhizobacteria and optimized according to superior community stability and Fusarium‐suppression capability, which surpasses the single strain and randomly formed microbiota. The optimized SynM (OptSynM) presents a distinctive cooperative pattern in which a key strain harbors the Fusarium suppression function by synthesizing the antagonistic substance fengycin, while other members intensify the functional performance by promoting the growth and the expression of the antagonistic and plant‐growth‐promoting related genes of the key strain. This study demonstrates innovative approaches to construct stable and minimal microbiota for sustainable agriculture and proposes a unique cooperative pattern to sustain community stability and functionality. [ABSTRACT FROM AUTHOR]