Soil respiration for a specific ecosystem can be characterized by its magnitude and its temporal and spatial variability. In order to accurately estimate carbon budgets in target ecosystems, we must be able to account for small-scale spatial variation in soil respiration. However, spatial heterogeneity of soil respiration has been less studied as compared with its magnitude and its temporal variability in agricultural ecosystems. Based on continuous measurement of soil respiration in a maize ecosystem in Northeast China from late April to late September in 2005, the spatial variation of soil respiration was elucidated and the effects of heat and water factors, soil properties, root biomass, and measurement position on it were analyzed synthetically. The results showed that there were significant spatial patterns for soil respiration at the plant scale of the maize ecosystem and higher soil respiration rates tended to occur near the maize plant during the growing season. The spatial variation of root biomass accounted for spatial heterogeneity of soil respiration, and there were linear relationships existing between soil respiration rate and root biomass. However, there were weaker relationships between the spatial heterogeneity of soil respiration and the spatial variation of other environmental factors such as the soil moisture, soil organic matter, total nitrogen content and C∶N. In addition, root respiration was evaluated indirectly by establishing linear regressive relationships between soil respiration rates and dry root weights. The contribution of root respiration to soil respiration averaged 54.5% and fluctuated from 43.1% to 63.6% during the maize-growing season.