The Jurassic climate change has attracted a great deal of attention from geologists. However, the investigations on the correlation between carbon isotopes of plant fossils and high CO2 levels in the Mesozoic are scarce. In this study, 16 well-preserved fossilized Ginkgoites and Phoenicopsis leaves were selected from the Xishanyao Formation in the Turpan basin. Two chemical protocols were applied for the pretreatment of stable carbon isotopes: HCl reagent and HCl + HF reagents. The average delta 13C values followed the two protocols were -22.8 %o and -22.9 %o, respectively, indicating that HF reagent has no effect on the carbon isotopes of the ginkgophyte fossils. The difference between the delta 13C values of Ginkgoites fossils and Phoenicopsis fossils is obvious, which is mainly caused by distinct carbon isotope fractionation between different plant taxa. However, both values show the same delta 13C trend in the early Middle Jurassic, i.e., increasing and then decreasing with time. In addition, both stomatal index (SI) and stomatal ratio (SR) methods are used to reconstruct paleo-CO2 levels with average values of 2564 ppmv and 1245 ppmv, respectively, indicating that SR method is more reliable. There was weak correlation (R = 0.23) between delta 13C and CO2 values in the early Middle Jurassic which may be due to low response of delta 13C values of ginkgophyte fossils to CO2 changes. Therefore, our work emphasizes the caution on using stable carbon isotopes of ginkgophyte fossils to reconstruct high paleo-CO2 concentrations.