Waterlogging damage is a key disaster threatening global crop yields. However, the impact of waterlogging stress on the growth and development of spring maize from the perspective of root-soil interaction is poorly understood. A pot experiment was conducted to explore the effects of waterlogging regimes on the root morphology, anaerobic respiration, rhizosphere soil enzyme activity, dry matter accumulation and yield of spring maize, as well as the recovery of each index after termination of waterlogging stress in 2019. The waterlogging regimes were performed for different durations (5, 10 and 15 days, respectively) at the seedling (V4) and heading (VT) stages, with non-waterlogging treatment as control (CK). Results showed that with the prolongation of waterlogging duration, root vigour, activities of invertase, urease, acid phosphatase and catalase in rhizosphere soil reduced, while the activities of lactate dehydrogenase, alcohol dehydrogenase and pyruvate decarboxylase in the anaerobic respiration pathway increased, also exacerbating the accumulation of lactic acid and ethanol, thereby reducing root length, root surface area, root activity and root dry weight. The greatest reductions in maize yield occurred at 15 days of waterlogging at the seedling and heading stages. Random forest analysis showed that root vigour was an important factor affecting root dry weight at the seedling and heading stages. The structural equation model showed that waterlogging durations and waterlogging regimes significantly affected root morphology and dry weight at the seedling stage rather than the heading stage, indicating that the seedling stage was more sensitive to waterlogging regimes than the heading stage. After the termination of waterlogging stress, maize roots recovered faster under short-term waterlogging stress than under long-term waterlogging stress. This study provided a theoretical basis for clarifying the adaptive mechanisms of crop roots under waterlogging stress.