To correlate the structural evolution of starch with its pasting properties under heat-shear, high-pressure homogenization (HPH) was applied near the gelatinization temperatures of three corn starches: waxy (WCS, 0:100), normal (NCS, 26:74), and high-amylose (HACS, 80:20). Structural analysis revealed a temperature-dependent degradation mechanism. Below gelatinization temperature, heat-shear follows a surface-to-core pattern, preserving the granule structure and the chain length distribution (CLD) of amylopectin. Within gelatinization temperature range, granule disintegration causes extensive chain scission, decreasing the weight-average molecular weight (Mw). The degradation pattern depends on the amylose/amylopectin ratio. In WCS (65 and 75 °C), cleavage targets the amylopectin backbone and inter-cluster chains (B2/B3). In NCS (67 and 77 °C) and HACS (71 and 91 °C), amylose potentially correlates with minor CLD changes in amylopectin. Collectively, these structural transformations drive a rheological shift: the starch paste transitions from elasticity-dominated to viscosity-dominated flow, evidenced by decreasing consistency index (K) and storage modulus (G′). This transition results from the loss of granule and crystalline structures, and the entanglement network formed by long-chain molecules (amylose and B2/B3 chains). Heat-shear processing provides mechanistic insights into designing starch pasting properties.