Three proton‐conductors, [Cu(5‐H2L)(IN)(H2O)]2H2[SiW12O40] ⋅ 2CH3CN ⋅ 2.5H2O (1), [Cu(4‐HL)(HIN)(H2O)]2H2[SiW12O40] ⋅ 7H2O (2) and [Cu(4‐HL)(HIN)(CH3CN)]2[HIN]2H4[PMo12O40]2 ⋅ 2CH3CN ⋅ 12H2O (3) (where 5‐H2L/4‐H2L is 5,5’/4,4’‐bis(hydroxymethyl)‐2,2’‐bipyridine and HIN is isonicotinic acid), were synthesized at room temperature. Interestingly, three dinuclear‐Cu(II)‐mixed‐organic‐ligand clusters, [Cu(5‐H2L)(IN)(H2O)]22+ cluster for 1, [Cu(4‐HL)(HIN)(H2O)]22+ for 2 and [Cu(4‐HL)(HIN)(CH3CN)]22+ for 3, are in situ synthesized under the coexistence of Keggin‐type polyoxometalates. More interestingly, in 1–3, the global Keggin‐type anions are well‐arranged in the hydrogen‐bonding networks of double‐Cu(II)‐mixed‐organic‐ligand clusters to give different spatial arrangement patterns. The [SiW12O40]4− anions in 1 display two dimensional layer pattern. The [SiW12O40]4− anions in 2 act as single bidentate O,O bridge ligands. The [PMo12O40]3− anions in 3 form the pair pattern. The AC impedance measurement results reveal 3 gives a high conductivity value over 10−3∼10−2 S ⋅ cm−1 in a wide temperature range from 25 to 100 °C under a wide relative humidity range from 35 to 98 %, while 1 and 2 give a middle conductivity value over 10−5∼10−4 S ⋅ cm−1 under the same conditions.