Improving the heat stability and functionality of whey protein isolate (WPI) is critical for its use in thermally processed foods. Maillard-type glycation with reducing polysaccharides is a promising approach to enhance solubility and reduce aggregation, but the role of carrageenan (CG) structure remains unclear. This study examined early-stage glycation of WPI with κ-, ι-, and λ-CG under wet-heating (70 °C, 0–12 h) at WPI:CG ratios of 10:1, 20:1, and 40:1. Glycation progression and structural changes were assessed by browning index, solubility, turbidity, transmittance, sulfhydryl content, surface hydrophobicity, SDS-PAGE, AFM, TEM, FTIR, and principal component analysis (PCA). The WPI/κ-CG 10:1 system at 6 h showed the highest browning index (1.45) and glycation degree (23.4%), surpassing ι-CG (16.9%) and λ-CG (13.1%) ( p < 0.05). κ-CG conjugates exhibited weaker high-molecular-weight bands on SDS-PAGE, compact nanostructures (40 nm) in AFM, and fewer irregular aggregates than λ-CG (100 nm). TEM confirmed that κ-CG effectively suppressed uncontrolled aggregation while maintaining dispersion. κ-CG also yielded the lowest hydrophobicity and sulfhydryl content, suggesting improved conformational stability. FTIR indicated stronger structural modification in κ-CG conjugates, moderate in ι-CG, and minimal in λ-CG. Solubility was significantly enhanced, reaching 98% at 6 h in the WPI/κ-CG 10:1 system ( p < 0.05). PCA showed κ-CG samples clustered with glycation and solubility markers, whereas λ-CG was associated with turbidity and limited modification. These findings demonstrated the structural dependence of CG in modulating Maillard glycation and demonstrate κ-CG as the most effective for stabilizing WPI, offering potential applications in protein-based beverages