We study discrete flavor symmetries of the models based on a ten-dimensional supersymmetric Yang-Mills (10D SYM) theory compactified on magnetized tori. We assume non-vanishing non-factorizable fluxes as well as the orbifold projections. These setups allow model-building with more various flavor structures. Indeed, we show that there exist various classes of non-Abelian discrete flavor symmetries. In particular, we find that S-3 flavor symmetries can be realized in the framework of the magnetized 10D SYM theory for the first time.