A novel mechanism for the nonlinear optical (NLO) effects of vanadium borate crystals, Na3VO2B6O11 (NVB), with distorted VO4 groups was investigated. A comprehensive analysis of the structure-property relationship was performed by combining the experimental measurements, the electronic structures calculations, the SHG-weighted electron density and the real-space atom-contribution analysis to yield the linear and nonlinear optical properties. The contribution of a (VO4)(3-) anionic group to the second harmonic generation (SHG) response was more pronounced than that of the (BO3)(3-) anionic group, which plays a virtual role in the SHG effects in NVB. The anionic (BO3)(3-) groups make dominant contributions to the birefringence, whereas the contribution of the V(5+) cations to these linear optical effects is negligible.