Two new hybrid organic–inorganic molybdates have been synthesized under ionothermal conditions, namely (H₄C₃N₂(C₆H₄N)₂N₂C₃H₄)²/_∞[Mo₁₁O₃₄]·H₂O (1), and (H₆C₅N(CH₂)₃NC₅H₆)¹/_∞[Mo₄O₁₃] (2), which were based on layered and chained _∞[Mo_nO_3n+1]²⁻ (n = 11, 4) blocks and two different sizes of organoammonium dications bis-(4-imidazol-1-yl-phenyl)-diazene and 1,3-di-(4-pyridyl)-propane (⁺HL1H⁺ and ⁺HL2H⁺), respectively. The ²/_∞[Mo₁₁O₃₄]²⁻ and ¹/_∞[Mo₄O₁₃]²⁻ units in 1 and 2 are unprecedented members of the _∞[Mo_nO_3n+1]²⁻ family with the new n value extended to 11 and 4, whose structure is similar with the _∞[MoO₃] slabs in α-MoO₃. Single crystal X-ray analysis shows that the _∞[Mo_nO_3n+1]²⁻ layers and chains in 1 and 2 are pillared in the three-dimensional (3D) networks by the organic dications, while the two connections at the organic–inorganic interface are similar. At the same time, the different _∞[Mo_nO_3n+1]²⁻ blocks (n = 11, 4) in hybrid organic–inorganic layered and chained molybdate materials are clearly evidenced by the efficient Raman spectroscopy. Moreover, the electrochemical impedance spectroscopy (EIS) measurements of 1 show a high conductivity (2.3 × 10⁻⁴ S cm⁻¹ at 75 °C and 90% relative humidity), with an activation energy of 0.45 eV for proton conduction. The mechanism of proton conduction for this molybdate material is proved to be Vehicular mechanism.