The development of thermally stable Type 5 resistant starch (RS5) is critical for functional food applications to modulate glycemic responses. This study investigated the structural assembly and enzymatic resistance of RS5 complexes prepared from high-amylose maize starch (HAMS) via a sequential strategy coupling pullulanase debranching with heat–moisture treatment (HMT). HAMS was debranched for varying durations (0–24 h) to generate short, linear glucan chains, subsequently complexed with myristic acid (MA) or linoleic acid (LOA), and further modified by pressure–heat treatment (PHT) or annealing (ANN). Extended debranching (24 h) significantly enhanced the complexing index and resistant starch (RS) content. While saturated MA promoted higher crystallinity of the hexagonal Bravais lattice, unsaturated LOA effectively enhanced resistance through steric hindrance despite lower crystallinity. Notably, PHT generally outperformed ANN, with the highest RS content (69.2%) achieved in DH24-LOA complexes treated at 120 °C with 10% moisture. Multi-scale structural analyses revealed that resistance originated from the transition of amorphous chains into highly ordered, thermally stable nanocrystals possessing a hexagonal Bravais lattice and the densification of the macroscopic architecture. These findings demonstrate that coupling pullulanase debranching with optimized PHT is a potent strategy to engineer high-performance RS5 ingredients with superior digestive resistance.