The first examples of lanthanide borate-acetate mixed anion compounds, namely, Ln2(CH3CO2)2[B5O9(OH)]·H2O (Ln = La 1; Ce 2; Pr 3), were synthesized under hydrothermal conditions. These compounds are isostructural and crystallize in polar space group Cc. They display a unique three-dimensional (3D) framework built by a 3D network of lanthanide borate further decorated by acetate anions. The borate anion exhibits a 2D layer in the ac plane with large 9-member rings (MRs) which are filled by lanthanide(III) ions into a {Ln[B5O9(OH)]}(-) 2D layer. Adjacent {Ln[B5O9(OH)]}(-) layers are bridged by remaining lanthanide (III) ions to form a 3D network of lanthanide borate. It is noteworthy that Ln2(CH3CO2)2[B5O9(OH)]·H2O (Ln = La 1; Ce 2; Pr 3) can be changed into Ln2(CH3CO2)2[B5O9(OH)] (Ln = La 4; Ce 5; Pr 6) under heating at 500 K. Compounds 1-4 display moderate SHG signals of about 2.0, 1.0, 1.4, and 2.5 times that of KH2PO4, respectively, and they are phase matchable. Their SHG responses mainly arise from the synergistic polarization effects of both asymmetric borate clusters and π-conjugated CH3COO(-) anions.