To enhance energy storage performance via modulation of crystal structure on the molecular level, two series of triethylamine (TEA)‐dependent polyoxometalate (POM) based inorganic‐organic hybrid compounds, [CuII(btx)2]2[SiW12O40] (SiW‐1), [CuI(btx)]4[SiW12O40] (SiW‐2), [CuI4(btx)3][SiW12O40] ⋅ 2H2O (SiW‐3), [{CuII6(btx)7(H2O)12}H4⊂(W12O40)2] ⋅ 12H2O (W‐1), [{CuII7(btx)8(H2O)10}H2⊂(W12O40)2] ⋅ 2H2O (W‐2) and [{CuII10CuI2(btx)11(H2O)16}H2⊂(W12O40)3] ⋅ 6H2O (W‐3) (btx=1,4‐bis(triazol‐1‐ylmethyl)benzene) have been synthesized and explored as pseudocapacitor electrode materials. Compared to other compounds, SiW‐2 shows a specific capacitance of 110.3 F g−1 at 3.0 A g−1 and only experiences a capacitance loss of 13 % after 1000 cycles at a current density of 18.0 A g−1. More importantly, the two series of compounds can be considered as a model for studying the effects of the molecular structures on the pseudocapacitor performance. The result verifies that besides the type of POM, the capacitance ability of the POM‐based compounds is mainly dominated by the connecting modes of adjacent POM building blocks and the dimension of covalent networks formed by POM building blocks. Thus, this work may open a new avenue to optimize the performance of POM‐based capacitors.