Adjusting birefringence to push the phase-matching (PM) of nonlinear optical (NLO) crystals blue-shifting to the deep-ultraviolet (DUV) region is the inorganic chemists and material scientists’ pursuit, while refractive dispersion as an important but easily overlooked optical properties generally brings the unexpected result. Herein, two new Y-based borates, K2YB3O6F2 and Rb2YB3O6F2 have been synthesized by the modulation of A-site cation. In both structures, owing to the structure-directing properties of Y-based polyhedra, the natural advantage of π-conjugated [B3O6] groups was pushed to the greatest extent, theoretical calculations and structure analysis revealed that the coplanar arrangement of [B3O6] groups results in the large birefringence of K2YB3O6F2 and Rb2YB3O6F2. Importantly, the aligned orientation of [B3O6] rings makes Rb2YB3O6F2 possess a strong SHG response of 5.0 × KDP, meanwhile the small dispersion of the refractive indices makes Rb2YB3O6F2 the first borate crystal containing the strong π-conjugation [B3O6] rings with the PM limit breaking through the ‘‘200 nm DUV wall’’. This work indicated that refractive dispersion can be effectively reduced through the cation effect, thereby broadening the PM range.