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BACKGROUND The formation of starch–lipid complexes is of interest to food processing and human nutrition. Fatty acid (FA) structure is important for the formation and structure of starch–FA complexes. However, there is limited research regarding the complexing behavior between amylose and different kinds of FAs, as well as the relationship between fine structures and digestibility of the formed complexes. This study aimed to investigate the behavior, fine structure, and digestibility of complexes formed between high amylose maize starch (HMS) and FA having various chain lengths and unsaturation degrees. RESULTS Complexes containing different FA structures showed V6III‐type crystals. Complexes containing 18‐carbon unsaturated FAs displayed significantly higher complexing index (P < 0.05) than other complexes. Complexes containing 12‐carbon FAs and 18‐carbon FAs with one unsaturation degree showed a higher degree of structural order and resistant starch (RS) content than other complexes. The 12‐carbon FAs exhibited a higher binding degree with helical cavity of amylose than other FAs. Additionally, 10‐carbon and 18‐carbon saturated FAs tended to combine with HMS outside amylose helices more than other FAs. Laser confocal micro‐Raman imaging revealed that the physically embedded 10‐carbon and 18‐carbon saturated FAs showed heterogeneous distribution in complexes, and that the complexed 18‐carbon FAs with one unsaturation degree exhibited homogeneous distribution. CONCLUSION The behavior, structural order and digestibility of complexes could be regulated by FA structure. The 12‐carbon FAs and 18‐carbon FAs with one unsaturation degree were more suitable for the production of HMS–FA complexes with higher structural order and RS content than other FAs. © 2022 Society of Chemical Industry.