Introducing F- anions or substituting F- anions with IO3- groups has been proven to be ideal strategies for designing novel noncentrosymmetric (NCS) and polar materials, yet systematic investigation into the effect of F- anions or the substitution of IO3- for F- anions on structures and properties remains rarely explored. Herein, two new gallium iodates, NaGa(IO3)2F2 (1) and NaGa(IO3)4 (2), were successfully designed and synthesized based on NaGa(IO3)3F by introducing more F- anions and replacing F- anions with IO3 groups, respectively. Structurally, in compound 1, the adjacent [GaF3(IO3)3]3- polyanions are connected in an antiparallel manner, resulting in a complete cancellation of local polarity. While in compound 2, all IO3 groups in 2D [Ga(IO3)4]∞- layers are aligned, leading to large macroscopic polarization. Additionally, chemical substitution also results in a qualitative improvement in the functional properties of compound 2. It possesses strong SHG response (12 × KDP @1064 nm) and broad optical transparency, coupled with large birefringence (0.21 @1064 nm), showcasing its promise as a promising nonlinear optical (NLO) crystal. The effects of chemical substitution between F- anions and IO3- groups on the structures and properties are discussed in detail.