By adopting two similar acyl thiourea‐based carboxylate ligands, 2‐(3‐benzoylthioureido)propionic acid (H3BTPA) and 2‐(3‐benzoylthioureido)ethanoic acid (H3BTEA) to react with Cu(OAc)2, respectively, one 2D cluster polymer [CuI6CuII6(BTPA)6(H2O)10]n (1) and one 0D cluster [CuI6CuII6(BTEA)6(H2O)10(DMF)2]⋅6H2O (2) (DMF=N, N‐dimethylformamide) were successfully prepared and structurally characterized. The optimized proton conductivity for 1 is 1.16 × 10−5 S⋅cm−1 under 98% RH and 100 °C, which can be increased to a higher value of 7.70 × 10−4 S⋅cm−1 under aqua‐ammonia vapor from 2.0 M of NH3⋅H2O solution. For 2, the largest proton conductivity of 9.80 × 10−4 S⋅cm−1 could be obtained under aqua‐ammonia vapor. Through PXRD determinations, water and ammonia adsorption measurements, Ea calculations, a clear understanding of their proton conduction mechanisms as well as the enhancement of aqua‐ammonia vapor on the proton conduction has been obtained.