Twist boundaries in the deep-UV nonlinear optical crystal KBe2BO3F2 (KBBF) are studied through first-principles calculations. It was found that the optical qualities and the capability for second-harmonic generation (SHG) in KBBF obtained from the different single-crystal growth methods are very different. These properties are associated with the presence of defects. Our studies demonstrate that the (0001) twist boundaries in KBBF are easily formed due to the quite weak interaction between the in-plane layers. These grain boundaries have very small influences on the modifications of the UV optical absorption edge and the refractive indices in KBBF. However, the SHG conversion efficiency in KBBF can be significantly deteriorated as the (0001) twist boundaries occur, so it is necessary to eliminate these twist boundaries during the single-crystal growth processes. Our theoretical results are consistent with experimental observations.