An asymmetric structure is the necessary requirement for second-order nonlinear-optical (NLO) materials, which have important applications in modern science and technology. Here we report two isostructural asymmetric compounds, RbBPO4F and CsBPO4F. Both compounds crystallize in cubic space group P2(1)3 (No. 198) with three-dimensional (3D) gismondine-like structures. Remarkably, in spite of the same basic structural units BO3F and PO4, both structures are distinct from the previously reported derivative KBPO4F, which crystallizes in a monoclinic space group Cc (No. 9) with a two-dimensional (2D)-layered structure. Careful structural analysis reveals that this structural transformation (from a monoclinic 2D structure to cubic 3D structures) should be aroused by the different alkaline ionic radii. To the best of our knowledge, such an abrupt structural transformation by alkaline elements is reported in all-inorganic asymmetric compounds for the first time. The structural transformation from 2D to 3D structures is favorable to eliminate the layered growth habit. This study will shed deep insight in the structural modulation of asymmetric compounds.