Moss biocrusts, as an important surface covering in dryland, are mainly distributed in patches. Patch size of moss biocrusts can significantly change the water content, evapotranspiration, and nutrient content of soil and mosses, and plays an important role in the stablity of desert surface and the carbon cycle. Rainfall is the main source of soil moisture in the desert, which can directly affect the physiological activity of moss and determine the carbon flux of moss biocrusts. However, it is not clear whether the response of carbon flux of moss patches with different sizes to rainfall is different? In this study, the dominant moss species (Syntrichia caninervis) of moss crusts in the Gurbantunggut Desert was selected to study the carbon flux of moss patches with different sizes (diameter:4.6 cm, 5.6 cm, and 10 cm) and was measured for 54 hours under different rainfall (0 mm, 2 mm, 5 mm, 15 mm rainfall). The results show that:(1) under the rainfall of 2 mm and 5 mm, the changing trend of net carbon exchange rate of moss with different patch sizes within 54 hours is similar. The cumulative carbon flux of patches with diameter of 4.6 cm and 5.6 cm is negative, which shows carbon fixation, while that of 10 cm patches shows carbon release on the contrary. Under the rainfall of 15 mm, the carbon flux of moss with different patch sizes shows carbon release. The changing trend of net carbon exchange rate of moss patch with a diameter of 10 cm with time is different from that of moss patch size with the diameter of 5.6 cm and 4.6 cm. (2) The changes of patch size and rainfall significantly affect the carbon flux of moss patches. The slope between soil water content and net carbon exchange rate increases with the increase of patch area. When the soil temperature is lower than 25℃, the carbon flux of moss patches decreases with the increase of soil temperature. When the soil temperature is higher than 25℃, the soil temperature has no significant effect on the carbon flux of moss patches. Therefore, the effects of rainfall and patch size on moss biocrust carbon flux should be considered in the future study of moss crust carbon flux in the desert. On the carbon budget balance, the result also explains that small moss patches have strong adaptability to desert small rainfall pulse. This study also provides a scientifically theoretical basis for evaluating the composition and distribution of moss patches and the carbon cycle of the desert ecosystem with the precipitation pattern change in the future.