To obtain new nonlinear optical (NLO) materials with a large second harmonic generation (SHG) effect has always been a great challenge. We have synthesized the first metal borate‐iodate NLO crystal, Be2(BO3)(IO3) (BBIO), by multicomponent modification of KBe2BO3F2 (KBBF), in which the structural features of KBBF were maintained and (IO3)− groups were connected to honeycomb [Be2BO3O2]∞ layers. As the first KBBF family member with mixed anionic groups, BBIO benefited from the synergistic effect of (IO3)−, (BO3)3− and (BeO4)6− groups, and exhibited a very strong SHG response of ≈7.2×KH2PO4 (KDP, @1064 nm) and a large birefringence (Δn) of 0.172 at 1064 nm. BBIO may, unexpectedly, optimize growth habits via van der Waals forces. This study presents borate‐iodate as a new NLO material and it demonstrates opportunities in KBBF structural engineering.