Soil respiration (Rs) plays an important role in the carbon cycle of terrestrial ecosystems. Understanding the impacts of plant community functional traits on Rs is a key prerequisite for accurate prediction of the future carbon balance of terrestrial ecosystems under climate change. This study examined the relationship of Rs with plants in the Ebinur Lake Basin in the arid desert region. Traditional statistical methods and geostatistical methods were used to study the spatial variation characteristics of Rs and to analyze the effects of plant community functional traits and environmental factors on the spatial heterogeneity of Rs. The variation in Rs in the arid desert area of the Ebinur Lake Basin showed a strong spatial dependence (C0/(C + C0) = 0.11) and a medium variation (α = 25.50, CV = 86.21%). Principal component analysis revealed that morphological traits of plants and soil water content had great contributions to PC1, soil nutrient had great contributions to PC2, and physiological traits of plants and soil temperature had large contributions to PC3. Multiple regression analysis showed that PC1, PC2, and PC3 can explain 83% of the spatial heterogeneity of Rs (F = 157.41, p < 0.01). In conclusion, maximum height, leaf width, leaf dry matter content, leaf thickness, and soil water content were the principal driving elements of soil respiration heterogeneity.