[Objective] The differences in soil respiration and its influencing factors between natural desert forest and farmlands were studied, in order to provide theoretical reference for the social development and ecological security maintenance in arid desert region.[Methods] Soil respiration rate and its influencing factors were investigated at three farmlands with different cultivation years (i. e., 30, 16, 3 years), and a natural desert forest in Ebinur Lake basin in the Xinjiang Uygur Autonomous Region. One-way ANOVA and multiple stepwise regressions were used for data analysis.[Results] ① Soil respiration rate increased significantly along the cultivation years (p<0.05). ② Soil respiration rate in three farmlands were signifiantly higher than that in natural desert forest (p<0.05). ③ Soil organic matter, soil moisture, total colony number, fine root biomass, soil salinity and pH value were significantly different between farmlands and natural desert forest (p<0.05), whereas there was no significant difference between soil temperature, air relative humidity and air temperature(p>0.05). ④ Soil moisture and salinity to soil respiration rate were the only remaining factores in the multiple stepwise regressions, and the standard coefficients were 0.67 and -0.42, respectively.[Conclusion] Agricultural activities increased soil moisture while decreased salinity in the reclaiming of natural desert forest into farmlands, and as a consequence, increased soil respiration rate along cultivation years.