Deep-UV coherent light generated by nonlinear optical (NLO) materials possesses highly important applications in photonic technologies. Beryllium borates comprising anionic planar layers have been shown to be the most promising deep UV NLO materials. Here, two novel NLO beryllium borates Na2Be4B4O11 and LiNa5Be12B12O33 have been developed through cationic structural engineering. The most closely arranged [Be2BO5](infinity) planar layers, connected by the flexible [B2O5] groups, have been found in their structures. This structural regulation strategy successfully resulted in the largest second harmonic generation (SHG) effects in the layered beryllium borates, which is similar to 1.3 and 1.4 times that of KDP for Na2Be4B4O11 and LiNa5Be12B12O33, respectively. The deep-UV optical transmittance spectra based on single crystals indicated their short-wavelength cut-offs are down to similar to 170 nm. These results demonstrated that Na2Be4B4O11 and LiNa5Be12B12O33 possess very promising application as deep-UV NLO crystals.