We study an approach to construct Siegel modular forms from Sp(6, Z). Zero-mode wave functions on T6 with magnetic flux background behave Siegel modular forms at the origin. Then T-symmetries partially break depending on the form of background magnetic flux. We study the background such that three T-symmetries TI, TII and TIII as well as the S-symmetry remain. Consequently, we obtain Siegel modular forms with three moduli parameters (ω1, ω2, ω3), which are multiplets of finite modular groups. We show several examples. As one of examples, we study Siegel modular forms for $$\widetilde{\Delta }\left(96\right)$$ in detail. Then, as a phenomenological applicantion, we study quark flavor models using Siegel modular forms for $$\widetilde{\Delta }\left(96\right)$$. Around the cusp, ω1 = i∞, the Siegel modular forms have hierarchical values depending on their TI-charges. We show the deviation of ω1 from the cusp can generate large quark mass hierarchies without fine-tuning. Furthermore CP violation is induced by deviation of ω2 from imaginary axis.