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• Waterlogging decreased starch granule size. • Waterlogging increased the proportion of long-chains and high-molecular-weight molecules in amylopectin. • Ordered structure of waterlogged starch decreased peak and breakdown viscosities. The grain formation stage is a critical stage that affects grain starch quality and frequently overlaps the rainy season in southern China for waxy maize production. Two waxy maize varieties were grown under control and waterlogging conditions during grain formation (1–15 days after pollination) to probe the effects of oversaturated soil moisture on starch structural and functional characteristics. Results indicated that waterlogging during grain formation decreased the size of starch granule, proportion of large granule (d > 15 μm) and ratio of medium-length chains (DP 10–24) in amylopectin, whereas the percentage of high-molecular-weight molecules were increased. Compared with the control, the percentage of ordered starch was increased by waterlogging for both varieties. The changes in starch internal structure under waterlogging had no influence on thermal stability, increased the maximum thermal decomposition ratio and pasting temperatures, and reduced pasting viscosity characteristics in both varieties. [ABSTRACT FROM AUTHOR]