Introducing F − anions or substituting F − anions with IO 3 − 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 IO 3 − for F − anions on structures and properties remains rarely explored. Herein, two new gallium iodates, NaGa(IO 3 ) 2 F 2 (1) and NaGa(IO 3 ) 4 (2), were successfully designed and synthesized based on NaGa(IO 3 ) 3 F by introducing more F − anions and replacing F − anions with IO 3 groups, respectively. Structurally, in compound 1, the adjacent [GaF 3 (IO 3 ) 3 ] 3− polyanions are connected in an antiparallel manner, resulting in a complete cancellation of local polarity. While in compound 2, all IO 3 groups in 2D [Ga(IO 3 ) 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 IO 3 − groups on the structures and properties are discussed in detail.