Non-centrosymmetric structure is the prerequisite to symmetry-dependent properties for functional materials. The inherent tendency of crystallization toward centrosymmetric arrangements has posed a great challenge in nonlinear optical crystals that requires non-centrosymmetric structure. Here we discovered two new hydroxyborates A[C(NH2)3][B4O5(OH)4]·nH2O (A = K, Rb; n = 3, 1.5), which have high similarity in cationic and anionic frameworks but clearly differ in terms of symmetry, such as non-centrosymmetric versus centrosymmetric. Variations in the hydrogen bonds of water molecules in the lattice are confirmed to be the origin of the symmetry breaking and transformation. The effectiveness of hydrogen bond-derived molecular engineering in producing non-centrosymmetric structure and opening up new avenues in the nonlinear optical crystal sector is demonstrated in this work.