Aims The objectives of this study were to investigate the effects of experimental warming on the fluxes of CO_2, CH_4 and N_2O of biological soil crusts (BSCs) and soil system, and to determine the relationships of the greenhouse gas fluxes with soil temperature and soil moisture. Methods We used open top chamber to imitate climate warming. Intact soil columns covered with three types of biological soil crusts, including moss, algae and mixed crusts of moss and algae, were collected at the southeast fringe of the Tengger Desert. The fluxes of CO_2, CH_4 and N_2O under warming and non-warming treatments were measured using static chamber and gas chromatography method during the period from July 2012 to June 2013. Important findings Warming and BSCs types had no significant effects on the fluxes of CO_2, CH_4 and N_2O. The CO_2 and CH_4 fluxes were significantly affected by sampling date as well as interactions between crust type and sampling date and among warming treatment, crust type and sampling date. An interaction between warming treatment and sampling date also significantly affected the CH_4 flux. However, no difference was found in the annual CO_2, CH_4 and N_2O fluxes and global warming potentials (GWP) in the three BSC types between the warming and non-warming treatments. CO_2 flux had a significant and positive exponential correlation with soil temperature at 5 cm depth and a significant and negative linear correlation with soil moisture at 10 cm depth. The CH_4 fluxes of moss and mixed crusts were significantly and negatively correlated with both soil temperature at 5 cm depth and soil moisture at 10 cm depth. No relationship was found between the N_2O flux and soil temperature, while the N_2O flux of moss crust was significantly and negatively correlated with soil moisture at 10 cm depth. Differences in CO_2 and CH_4 fluxes of moss crust between the warming and non-warming treatments were significantly and negatively correlated with the difference of soil temperature at 5 cm depth between the two treatments; whereas the difference in N_2O flux of algae crust was marginally and positively correlated (p = 0.051) with the difference in soil temperature. All results mentioned above suggest that the fluxes of greenhouse gases would not experience a significant change for the BSCs-soil system under global warming, meaning that the feedback of greenhouse gases in the desert ecosystem to climate warming would not be large in the future.