During the controllable synthesis of two vanadium-containing Keggin-type polyoxoniobates (PONbs), [Ni(en)2]5[PNb12O40(VO)5](OH)5·18H2O (1) and [Ni(en)3]5[PNb12O40(VO)2]∙17H2O (2, en = ethylenediamine) are realized by changing the vanadium source and hydrothermal temperature. Compounds 1 and 2 have been thoroughly characterized by single-crystal X-ray diffraction analysis, FT-IR spectra, X-ray photoelectron spectrum (XPS), powder X-ray diffraction (PXRD), etc. Compound 1 contains a penta-capped Keggin-type polyoxoniobate {PNb12O40(VO)5}, which is connected by adjacent [Ni(en)2]2+ units into a three-dimensional (3D) organic-inorganic framework, representing the first nickel complexes connected vanadoniobate-based 3D material. Compound 2 is a discrete di-capped Keggin-type polyoxoniobate {PNb12O40(VO)2} with [Ni(en)3]2+ units as counter cations. Compounds 1 and 2 have poor solubility in common solvents and can keep stable in the pH range of 4 to 14. Notably, both 1 and 2 as electrode materials are active for the selective oxidation of benzyl alcohol to benzaldehyde. Under ambient conditions without adding an alkaline additive, compound 1 as a noble metal free electrocatalyst can achieve 92% conversion of benzyl alcohol, giving a Faraday efficiency of 93%; comparatively, 2 converted 79% of the substrate with a Faraday efficiency of 84%. The control experiments indicate that both the alkaline polyoxoniobate cluster and the capped vanadium atoms play an important role during the electrocatalytic oxidation process.