We consider a composite Higgs model based on the $SU(6)/Sp(6)$ coset, where an $U(1)$ subgroup of $Sp(6)$ is identified as the flavor symmetry. A complex scalar field $s$, which is a pseudo-Nambu-Goldstone boson of the broken symmetry, carries a flavor charge and plays the role of a flavon field. The $U(1)_F$ flavor symmetry is then broken by a VEV of the flavon field, which leads to a small parameter and generates the mass hierarchy between the top and bottom quarks. A light flavon below the TeV scale can be naturally introduced, which provides a fully testable model for the origin of flavor hierarchy. A light flavon also leads to substantial flavor changing neutral currents, which are strongly constrained by the flavor precision tests. The direct search of additional scalar bosons can also be conducted in HL-LHC and future hadron colliders.

12 pages, 1 figure, 3 tables; v2: two appendices added, matches version accepted for publication in PRD