In order to understand the controlling environmental factors of soil organic carbon cycling in the lower reaches of the Tarim River, we studied daily variation of soil respiration and its relationship with air temperature at 10 cm above ground surface and soil water contents in riparian forests in sections of Karerdayi and Alagan. Measurements of soil respiration were made with a LI-8100 soil CO₂ efflux system. Nonlinear regression analysis was performed with SPSS13.0. We observed that: (1) the daily variation of soil respiration was fairly consistent between Populus euphratica and Tamarix spp. communities, with diurnal variation curve of soil CO2 emissions displaying a single peak and the maximum rate of soil CO2 efflux occurring at the same time; (2) the timing for the occurrence of maximum rate of soil CO₂ efflux varied monthly; (3) the rates of soil respiration under the forests of Populus euphratica was significantly greater than under the forests of Tamarix spp.; (4) an exponential model can be used to describe the relationship between soil respiration and air temperature at 10 cm above ground surface, with the sensitivity of soil respiration to temperature differing between different vegetation types; (5) a liner model can better describe the relationship between soil respiration and soil water content; and (6) air temperature at 10 cm above the ground surface and soil water content together controlled the rates of soil respiration and explained 76%～93% of the variance in desert riparian forests of the lower reaches of Tarim River.