Sedimentary Fe deposits are both scientifically and economically important. As a major ore mineral of these deposits, siderite is generally assumed to have been formed via diagenetic transformation of other Fe-bearing minerals. The Devonian Daxigou sedimentary siderite deposit, Central China, contains ca. 500 Mt Fe with an average ore grade of ca. 30 wt% FeO^T but is poorly known in the literature. Different from most sedimentary Fe deposits that contain multiple generations of Fe-bearing minerals, the ore mineral in this deposit is solely siderite, and thus may provide valuable information about the processes of siderite mineralization. Stratiform orebodies of the Daxigou deposit are hosted in a turbidite sequence formed in the Devonian Zhashui-Shanyang intraplate rift basin. Orebodies are composed of interbedded ore and mudstone layers. The ore mineral is siderite and gangue minerals are quartz and clay minerals (mainly muscovite and illite). Siderite has shale-normalized REE+Y patterns with positive Eu anomalies (Eu/Eu*_PAAS = 1.19–1.59) and low Y/Ho ratios (Y/Ho = 27.5–32.6) indicative of involvement of seafloor hydrothermal fluids. Siderite separates have εNd_(t) values from − 9.9 to -8.9, suggesting that Fe was leached from underlying clastic rocks. Siderite has δ¹³C_PDB values from − 3.45 to -1.09‰ and δ⁵⁶Fe_IRMM014 values from − 0.72‰ to -0.27‰, with only limited fractionations relative to dissolved inorganic carbon in seawaters and to hydrothermally derived Fe²⁺. High resolution transmission electron microscopic images reveal that siderite grains were nucleated on the surface of clay minerals. Thus, we conclude that siderite of the Daxigou deposit was precipitated directly from ferruginous seawaters via heterogeneous nucleation on clay minerals at elevated temperatures, instead of formation through diagenetic transformation from other Fe-bearing minerals. The Daxigou deposit can be considered as a unique primary sedimentary siderite deposit. It was formed under an extensional regime of the South China Craton during the breakup of Gondwana. Our study provides new insights about the mineralization pathways of sedimentary Fe deposits in the geological past.