A novel noncentrosymmetric calcium borate, Ca-2[B5O9].(OH).H2O (1), was synthesized under solvothermal condition using mixed solvents of pyridine and H2O. Compound 1 crystallizes in the monoclinic space group Cc. Its structure contains [B5O12] units and features a three-dimensional (3D) pcu net with nine-membered ring (9-MR) channels along the b-axis, where the Ca2+ cations, OH- ions, and H2O molecules are located. Each Ca polyhedron shares three edges and one vertex with four neighbors to form a 3D dia Ca-O network. The pcu B-O net and dia Ca-O net are further interpenetrated to give the final denser net. The second harmonic generation (SHG) measurement shows that compound 1 is a type I phase-matchable material with a strong SHG response of similar to 3 times that of KH2PO4. In addition, it exhibits a wide transparency range with a short UV cutoff edge below 200 nm. These results reveal that the compound is a potential deep-UV nonlinear optical material. The Vienna ab initio theoretical studies indicate the good SHG response is derived from the synergistic effect of the p-conjugated systems of BO3 groups and distorted CaO9 polyhedra.