We consider magnetized orbifolds, where the supersymmetric mass term for a pair of up- and down-type Higgs (super)fields, called $mu$-term, is localized at the orbifold fixed points, and study the effects on the zero-mode spectra. The zero-mode degeneracy to be identified as the generation in four-dimensional (4D) effective theories is determined by the magnetic fluxes. It is known that multiple Higgs zero-modes appear in general in magnetized orbifold models. We derive the analytic form of the $mu$-term matrix in the 4D effective theory generated by the localized sources on $T^2/Z_2$ orbifold fixed points, and find that this matrix can lead to a distinctive pattern of the eigenvalues that yields hierarchical $mu$-terms for the multiple Higgs fields. The lightest ones can be exponentially suppressed due to the localized wavefunctions of zero-modes determined by the fluxes, while the others are of the order of the compactification scale, which can provide a dynamical origin of the electroweak scale as well as a simultaneous decoupling of extra Higgs fields. We also show that a certain linear combination of the lightest Higgs fields could generate the observed mass ratios of down-type quarks through their Yukawa couplings determined by the wavefunctions.
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