Sugarcane (Saccharum officinarum L.), an intensive, long-term, monoculture, economical crop in South Africa, is known to degrade soil characteristics. Soil structure, a key indicator of soil health and biomass production potential, is manageable by agricultural practices. This study aims to evaluate the effect of crop residue management practices (mulching, burning with residues scattered or removed) and mineral fertilization (with or without) on soil structure by analyzing soil shrinkage curves (SSCs) and other soil physical and chemical properties in a long-term sugarcane trial established in 1939. The SSC provides descriptive structural soil data by differentiating and characterizing two pore systems (plasma and structural pores). By analyzing the SSC of 24 plots (four replicates each treatment), residue management and fertilization practices were found to have statistically and physically significant effects on hydrostructural variables. Partial redundancy analysis showed that residue management practices had a slightly higher effect (19/100 of total variance) on hydrostructural variables compared with fertilization (12/100). The main hydrostructural variables representing the management effect were total soil shrinkage, specific volume, and swelling capacity of the plasma, which were higher in mulched and/or unfertilized plots, indicating that soil was less compact, and shrinkage was more intense, including at the plasma level. The stronger structural dynamics and aggregate stability of the soil were explained by the behavior of the primary aggregates (peds), which were more porous and reactive during the drying process. This study highlights the importance of mulching and limited fertilization to maintain soil structure in the long term while still ensuring yield production.