This study aimed to visualize the microstructures of starch hydrogels using synchrotron-based X-ray micro-computed tomography (μCT). Waxy maize starch (WMS, 3.3% amylose, db), pea starch (PS, 40.3% amylose), and high-amylose maize starch (HMS, 63.6% amylose) were cooked at 95 and 140 °C to prepare starch hydrogels. WMS and HMS failed to form a gel after 95 °C cooking and storage, while PS developed a firm gel. At 140 °C cooking, HMS of a high amylose nature was fully gelatinized and generated a rigid gel with the highest strength. Both scanning electron microscopy (SEM) and μCT revealed the unique structural features of various starch hydrogels/pastes prepared at different temperatures, which were greatly affected by the degree of swelling and dispersity of the starches. As a nondestructive method, μCT showed certain advantages over SEM, including minimal shrinkage of the hydrogels, relatively simple sample preparation, and allowing for three-dimensional reconstruction of the hydrogel microstructure. This study indicated that synchrotron-based μCT could be a useful technique in visualizing biopolymer-based hydrogels.