In this paper, we investigate the geometry and classification of three-dimensional CR Yamabe solitons and pseudo-gradient CR Yamabe solitons. In the compact case, we obtain a classification result of three-dimensional CR Yamabe solitons under the assumption that their potential functions are in the kernel of the CR Paneitz operator. In addition, we obtain a structure theorem on the diffeomorphism types of complete three-dimensional pseudo-gradient CR Yamabe solitons (shrinking, steady, or expanding) of vanishing torsion.