Multi-point root zone micro-irrigation (MRMI) is a promising technology for precision water management, particularly for shallow-rooted crops in soils with high water-holding capacity. Aiming to address the weak stress tolerance of shallow root systems in native macadamia trees, a condition resulting from low-phosphorus strategies. By utilizing the high water-holding capacity of Yunnan red soil, a targeted, 4-point spatial micro-irrigation strategy was proposed and validated to steer and remodel root morphology in seedlings. Field greenhouse experiments indicated that under a time-differentiated irrigation regime (The total daily irrigation amounts were 1.08 mm, 0.83 mm, and 0.58 mm for months of 0~4, 5~8, and 9~12, respectively.), both MRMI and surface drip irrigation (SDI) created vertical soil moisture gradients. However, the gradients under MRMI were more stable and concentrated. At 1.08 mm and 0.83 mm application rates, MRMI established a suitable soil moisture range (0.30~0.35 cm3/cm3) in the middle and deep layers (20~40 cm). At the 0.58 mm rate, the 40 cm soil layer also remained consistently within this range, thereby creating effective moisture-driven conditions for horizontal expansion and deep vertical penetration of the roots. At the 12th month, root sample metrics showed that indicators for MRMI in the shallow and deep layers were significantly different from those for SDI (p<0.01), while root length density (RLD) and root volume (RV) in the middle layer showed significant differences (p<0.05). Compared with SDI, MRMI reduced the horizontal spread of the root system by 17.95% while increasing its vertical penetration depth by 23.53%. This fostered the evolution of a multi-tiered, near-bell-shaped root architecture, characterized by moderate horizontal spread and significant vertical penetration, which enhanced the root system’s dual capacity for absorbing both soil water and nutrients. The research presented an innovative irrigation-based strategy to overcome morphological defects in crop roots, offering new insights for cultivating stress tolerance in shallow-rooted, sparsely planted crops.