High amylose maize starch (HAMS) was extracted using sodium hydroxide (NaOH), sodium bisulfite (Na₂SO₃), and sodium metabisulfite (Na₂S₂O₅) under 25, 50, and 70 °C, respectively. This study identified the optimum HAMS extraction methods with the lowest protein and lipid content and investigated the effect of extraction methods on the molecular and lamellar structures of HAMS. Higher temperature (50 and 70 °C) improved the purity of starch but reduced the averaged chain length (ACL) of amylose and the thickness of crystalline layers in lamellar structure. Low temperature caused less molecular degradation of starch but resulted in higher contents of protein and lipid adhering to the HAMS. Extraction using NaOH at 50 °C gave the highest purity, whereas the long chains of starch were degraded. Taking all factors into account, soaking high amylose maize grain in Na₂SO₃ at 50 °C was chosen, since it produced purer starches with lower protein and lipid content compared with other two temperatures (25 and 70 °C) and alkalis (NaOH and Na₂S₂O₅), and the starches were less affected in structure and physical properties. This result is very useful for HAMS extraction and processing.