It is crucial to find a convenient and sensitive method for quantitative determination of heavy metal chromium(VI) ions. Developing crystalline materials coupled with polyoxometalates as an electrochemical sensor is a promising approach to address the above issues. Here we reported two reductive polyoxometalate-based crystalline compounds with the formula of (H₂bpp)₂[Na₄Fe(H₂O)₇][Fe(P₄Mo₆O₃₁H₆)₂]·2H₂O (1) and (H₂bpp)₆(bpp)₂[Fe(P₄Mo₆O₃₁H₈)₂]₂·13H₂O (2) (bpp = 1,3-bi(4-pyridyl)propane). Structural analysis indicated that both two compounds were composed of inorganic polyanionic clusters and organic protonated bpp cations. The difference lies in the arrangement mode of the inorganic moiety: crystal 1 shows a unique three-dimensional (3-D) inorganic porous skeleton, while crystal 2 consists of isolated 0-D polyanionic clusters. When used as electrochemical sensors in the determination of trace Cr(VI), crystal 1 shows a broad linearity range (2–2610 μM) with a low limit of detection (LOD) of 0.174 μM (9 ppb), which is superior to that of compound 2 (a LOD of 0.33 μM) and meets the standard of Cr(VI) in drinking water set by the WHO (less than 0.962 μM or 50 ppb). Importantly, crystal 1 showed benign selectivity to Cr(VI) in the presence of various heavy metal ions and good reproducibility in a real water sample, which prove its strong anti-interference ability. In addition, experimental results showed that the spatial arrangement of polyanionic clusters could affect the final electrochemical behavior of crystalline materials. This work provides some insights into the design of cost-effective POM-based electrochemical sensors at the molecular level.