Although the micropaleontology of Ordovician deep-sea cherts is relatively well documented, microfossil assemblages in Ordovician shallow-marine cherts are less well-known. Nodular cherts in the Middle Ordovician carbonates of the Yijianfang Formation (Well YJ1X) in the Tarim Basin, northwestern China, contain a rich microfossil assemblage deposited in a shallow marine setting. These cherts contain 11 genera and 13 species of acritarchs and filamentous cyanobacteria. The acritarch assemblage includes eight genera and eight species, namely, Aremoricanium sp., Cheleutochroa oculata, Cymatiogalea sp., Cymatiosphaera sp., Dictyotidium microreticulatum, Leiosphaeridia sp., Polygonium gracile, and Pterospermella sp. Filamentous cyanobacteria include two genera and four species, namely, Siphonophycus typicum, Siphonophycus kestron, Siphonophycus solidum, and Oscillatoriopsis longa, and a colony of Eoentophysalis sp. coccoidal cells. The acritarch assemblage indicates a Middle-Late Ordovician age. The Yijianfang Formation fossil assemblage indicates a deep offshore depositional environment. Sedimentological evidence also suggests that the limestone that hosts the chert interval was deposited in a low- to moderate-energy, restricted, inner carbonate platform. Cherts formed by silicification during late diagenesis. By complementing previous studies of acritarchs in shales, this work improves the understanding of the Middle Ordovician paleogeography and microbial world.