Fossil Ginkgophyta are one of the most widely used indicators for estimating the paleoatmospheric CO2 levels from the Triassic to present day. There are quite a few CO2 estimates for the Triassic to Jurassic interval; however, the data from China are still limited. In this study, two fossil Ginkgoites species, Ginkgoites magnifolius Du Toit and Ginkgoites obrutschewii (Seward) Seward, are described based on recent collections from the Upper Triassic and Middle Jurassic in Huating County, Gansu Province, Northwest China. The fossil leaf morphology and epidermal structure were studied and the stomatal parameters were analyzed for the reconstruction of paleoatmospheric CO2 concentrations. The paleoatmospheric CO2 concentration during the Late Triassic of China is estimated for the first time based on fossil material from Gansu. Our fossils yield paleo-CO2 values of 1962 ppmv in the Late Triassic and 1320 ppmv in the Middle Jurassic. Compared with previous estimates of atmospheric CO2 concentration based on stomatal parameter of fossil Ginkgo/Ginkgoites from Northwest China, the change of Jurassic paleo-CO2 levels accord with the trend of CO2 concentration proposed by GEOCARB III and Crustal Production models. The results demonstrate that the paleo-CO2 of the Late Triassic was higher than that of the Early to Middle Jurassic; but an increasing trend of paleo-CO2 could be detected from the Early to the Middle Jurassic. However, the GEOCARBSULF model indicates a decreasing trend during this interval. Therefore, the present data provide an independent check for the paleo-CO2 value estimation based on isotopic analysis.