Understanding the mechanisms of interannual variations (IAVs) in cropland respiration (ER) can aid in optimizing field management strategies and accurately assessin bon budget. The long-term carbon exchange over a (winter) wheat-(summer) maize double-cropping system was measured with the eddy covariance technique to identify the IAVs in ER and the influencing factors, and investigate whether field management strategy (crop residue retuning) affects ER. Results showed that the growing season-related ER values for wheat (w-ER) and maize (s-ER) ranged from 471.77 to 681.96 g C m⁻² y⁻¹ and from 433.91 to 826.89 g C m⁻² y⁻¹, respectively, during 2007–2012. Pearson’s correlation analysis indicated that the IAVs in w-ER were controlled by the crop residual carbon levels for maize from the prior season (s-C_r) and the gross ecosystem productivity. The seasonal mean air temperature (T_a) and maximum leaf area index for maize were found to be factors affecting the IAVs in s-ER. Because of the high correlation between the controlling factors, path analysis was used to deconvolute their respective contributions to the IAVs in ER. Integration analysis of path coefficients showed that s-C_r and T_a were the primary influencing factors, because they explained approximately 81% and 68% of the IAVs in ER for wheat and maize, respectively. Overall, our findings highlighted the importance of crop residue management for agroecosystem carbon cycling, but its effects may depend on ecosystem types.