Baked milk is subjected to prolonged high-temperature processing, which often undermines its dispersion stability. While carrageenan is known to inhibit milk demixing, its role in stabilizing heat-induced protein aggregates remains inadequately understood. In this study, we isolated casein micelles (CM), whey protein-casein aggregates (WPCA), and whey protein aggregates (WPA) from baked milk through centrifugation. LC-MS/MS analysis revealed that the addition of 0.02% carrageenan prior to baking significantly reduced whey protein aggregation, markedly reducing WPA and WPCA. We quantitatively assessed the adsorption patterns of carrageenans of varying molecular weights and types. Results suggested that λC were predominantly nonadsorbing, enhancing system stability through thickening. Conversely, ιC demonstrated non-selective adsorption onto both CM and WPCA, while κC primarily targeted WPCA. Furthermore, longer chains of carrageenan might inhibit the formation of insoluble complexes with WPCA. This research provides valuable insights for understanding the stabilization mechanisms of carrageenans in real processing within milk systems.