In recent years, an increasing number of plant fossil leaves and petrified woods have been discovered from the Middle Jurassic Wanbao Formation in Moguqi Town of Inner Mongolia, NE China. Here, we describe a new species of Coniopteris moguqiensis sp. nov. preserved as a fragment with fertile and sterile pinnules. The sterile ultimate pinnules are elongate ovate with sphenopteriod type venation, and fertile pinnules are usually isolated, bipinnate at least with the sorus apical, elliptical, 1 mm in diameter; sporangia are almost globular, 100–150 μm in diameter, and the annulus is vertical. In situ spores are rounded-triangular in polar view, 25–30 μm in diameter with sides straight and slightly convex; trilete, laesurae are thin and slightly straight; the exine surface is usually psilate under the light microscope but finely reticuloid sculptured on the proximal view under a scanning electronic microscope. The fern genus Coniopteris usually suggests a warm and humid environment, which is consistent with the palaeoclimatic conditions of petrified wood and megafossil plants. The new discovery further supplements the floral composition of the Wanbao Formation, providing new material for understanding the evolutionary trend and classification of Coniopteris.