Well-preserved Ginkgo pollen organs are analyzed from the Middle Jurassic Xishanyao Formation of the Turpan–Hami Basin, Xinjiang Uygur Autonomous Region, northwestern China, and are described as a new species, Ginkgo hamiensis Z.X. Wang et B.N. Sun sp. nov. The immature male cones are cylindrical and catkin-like, with two longitudinal stripes on the stalk. The pollen sacs are shaped like a long oval with two pollen sacs fused together for each microsporophyll, and the microsporophyll tip is a triangular cystidium. The pollen grains are oblong or fusiform and monocolpate; both ends are blunt or sharp. By comparison with previously reported fossil records of Ginkgo plants, we determined that the current fossils are different from all other reported species; thus, the present fossil is referred to as a new species of Ginkgo. The reproductive organs of the Ginkgo fossils described herein can provide valuable information for the study of Ginkgo plants. Further, there are two probable evolutionary trends in the Ginkgo pollen cones. One trend is that the number of pollen sacs changed from three or four during the Jurassic and Cretaceous to two at the present day; the other is that the number of pollen sacs has remained two from the Middle Jurassic to the present day. In addition, the pollen cones described herein are similar to the pollen cones of the extant Ginkgo, which strongly indicates that the morphology of Ginkgo plants may have remained highly conserved over millions of years.