Fluorooxoborates, as a newly found and promising deep-UV nonlinear optical (NLO) system, have exhibited superiority in optical performance. An in-depth study of the relationship among the symmetry, structure, and properties is urgently needed. Here, we studied the influence of the fluorooxo-functional units in typical fluorooxoborates. The symmetry of the fluorooxo-functional units is identified for the first time, and the fluorooxo-functional unit can play a great role in the symmetry breaking. The influence of the fluorooxo-functional units on the second harmonic generation (SHG) response was explored. Definitive evidence observed from the crystal orbital Hamilton population and band-resolved analysis illustrates the contribution of the antibonding of B-F to the SHG in the valence bands near the Fermi level. This work provides useful insights in the important contribution of the fluorooxo-functional units to SHG response, enabling the rational design of fluorooxoborate NLO materials with high performance.