Visible‐light‐driven photocatalytic Cr(VI) reduction is a promising pathway to moderate environmental pollution, in which the development of photocatalysts is pivotal. Herein, three hourglass‐type phosphomolybdate‐based hybrids with the formula of: (H2bpe)3[Zn(H2PO4)][Zn(bpe)(H2O)2]H{Zn[P4Mo6O31H6]2} ⋅ 6H2O (1) Na6[H2bz]2[ZnNa4(H2O)5]{Zn [P4Mo6O31H3]2} ⋅ 2H2O (2) and (H2mbpy) {[Zn(mbpy)(H2O)]2[Zn(H2O)]2}{Zn[P4Mo6O31H6]2} ⋅ 10H2O (3) (bpe=trans‐1,2‐bi(4‐pyridyl)‐ethylene; bz=4,4′‐diaminobiphenyl; mbpy=4,4’‐dimethyl‐2,2’bipyridine) were synthesized under the guidance of the functional organic moiety modification strategy. Structural analysis showed that hybrids 1–3 have similar 2D layer‐like spatial arrangements constructed by {Zn[P4Mo6]2} clusters and organic components with different conjugated degree. With excellent redox properties and wide visible‐light absorption capacities, hybrids 1–3 display favourable photocatalytic activity for Cr(VI) reduction with 79%, 70% and 64% reduction rates, which are superior to that of only inorganic {Zn[P4Mo6]2} itself (21%). The investigation of organic components on photocatalytic performance of hybrids 1–3 suggested that the organic counter cations (bpe, bz and mbpy) can effectively affect the visible‐light absorption, as well as the recombination of photogenerated carriers stemmed from {Zn[P4Mo6]2} clusters, further promoting their photocatalytic performances towards Cr(VI) reduction. This work provides an experimental basis for the design of functionalized photocatalysts via the modification of organic species.