A series of ammonium-containing fluoroiodates, NH4IO2F2 and (NH4)3(IO2F2)3·H2O, with isolated [IO2F2] units have been fabricated by a fluorine-oxygen substitution strategy from NH4IO3. The two compounds crystallize in the orthorhombic system, but in different space groups, noncentrosymmetric Pca21 for NH4IO2F2 and centrosymmetric Pnma for (NH4)3(IO2F2)3·H2O, and show wide band gaps of 4.53 eV for (NH4IO2F2) and 4.55 eV for ((NH4)3(IO2F2)3·H2O). In addition, NH4IO2F2 exhibits a 1.2 × KDP second harmonic generation response, a short ultraviolet cutoff edge in iodates, and a good crystal growth habit. The crystal of NH4IO2F2 with a size of 11 × 5 × 2 mm3 was obtained by the aqueous solution method. The results enrich the structural diversity of iodate and supply a greater understanding of the design of new functional materials based on the fluoroiodates.