Three new nickel-cluster-substituted polyoxometalates (POMs), [Ni6(H2O)9(μ3-OH)3(HSiW9O34)]2·12H2O (1), [Ni(en)(H2O)3][Ni6(H2O)3(en)2L(μ3-OH)3(HSiW9O34)]2·9H2O (2) (en = ethylenediamine; L = C7H5O2 = benzoic acid) and [Ni6(L')6(CH3COO)(H2O)3(μ3-OH)3(HPW9O34)]2·9H2O (3) (L' = C5NH5 = pyridine) were successfully isolated under hydro-/solvothermal conditions. 1-3 were structurally characterized by single-crystal XRD, elemental analyses, PXRD, IR, and TGA. Compound 1 mainly consists of a pair of {Ni6SiW9} fragments and some water molecules. Interestingly, the whole structure can be regarded as the connection of {Ni6SiW9} and another unit rotated 180° through Ni-O-W bonds, forming a dimeric structure {Ni6SiW9}2. Compounds 2 and 3 also have an {Ni6XW9}2 (X = Si, P) dimer, but there is a big difference in the connection between {Ni6SiW9} units. On this basis, mono-dentate conjugated organic ligands (benzoic acid (L) and pyridine (L')) were successfully introduced. It is noteworthy that pyridine molecules were first integrated into {Ni6SiW9}-based clusters and 3 features the highest number of organic ligands (six pyridines per Ni6) in the reported {Ni6XW9}-based clusters. The introduction of organic ligands to compounds 2 and 3 can bring about better third-order nonlinear optical properties. Magnetic research indicated the existence of ferromagnetic interactions in 2-3.