The chain reorganization of cooked starch during storage plays an important role in the performance of starchy products such as rice foods. Here, different analytical techniques (such as small-angle X-ray scattering) were used to reveal how microwave cooking influences the chain assembly of cooked indica rice starch undergoing storage for 0, 24, or 48 h. While stored, more short-range double helices, long-range crystallites, and nanoscale orders emerged for the microwave-cooked starch than for its conventionally cooked counterpart. For instance, after storage for 24 h, the microwave-cooked starch contained 46.8% of double helices, while its conventionally cooked counterpart possessed 34.3% of double helices. This could be related to the fact that the microwave field caused high-frequency movements of polar groups such as hydroxyls, which strengthened the interactions between starch chains and water molecules and eventually their assembly into double helices, crystallites, and nanoscale orders. This work provides further insights into the chain reassembly of microwave-cooked starch undergoing storage, which is closely related to the quality attributes of starch-based products.