Digestion properties were investigated for sodium alginate-high amylose corn starch–conjugated linoleic acid ternary complex (AG-HACS-CLA). The in vitro digestion properties of AG-HACS-CLA were measured by the hydrolysis curve method, the crystal structure of AG-HACS-CLA was determined by X-ray diffractometer and Fourier-transform infrared spectrometer analyses, and the relationship between the digestion properties and crystal structure of the complex were explored. The results showed that before gelatinization and pasting, AG-HACS-CLA was a low glycemic index food with a predicted glycemic index (pGI) of 47.06, while the gelatinized and pasted AG-HACS-CLA was a medium glycemic index food with a pGI of 58.27. The in vitro digestion properties of AG-HACS-CLA were influenced by the type of crystal and degree of crystallization, and the resistant starch content of AG-HACS-CLA was related to the microcrystal phase. A V-type crystal with a high degree of order was formed after the complexation of starch with CLA, so that the proportion of the microcrystal phase in AG-HACS-CLA increased by 3.5%, compared to the sample without addition of CLA. Compared to the natural HACS, with a B-type crystal structure, AG-HACS-CLA exhibited better structural stability and greater resistance to digestion. AG prevented the formation of intermolecular hydrogen bonds in AG-HACS-CLA. The proportion of AG-HACS-CLA in the microcrystal phase was decreased by 7.1% and the content of resistant starch in AG-HACS-CLA was decreased by 20% compared to that of the sample without addition of AG.