GEMS-0067 (PI 643420) maize line is a homozygous mutant of the recessive amylose-extender (ae) allele and an unknown number of high-amylose modifier (HAM) gene(s). GEMS-0067 produces starch with a approximately 25% higher resistant-starch (RS) content than maize ae single-mutant starches. The objective of this study was to understand how the HAM gene(s) affected the RS content and other properties of ae-background starches. Nine maize samples, including G/G, G/F1, G/H, F1/G, F1/F1, F1/H, H/G, H/F1, and H/H with HAM gene-dosages of 100, 83.3, 66.7, 66.7, 50, 33.3, 33.3, 16.7, and 0%, respectively, were produced from self- and intercrosses of GEMS-0067 (G), H99ae (H), and GEMS-0067xH99ae (F1) in a generation-means analysis (GMA) study. RS contents of examined starches were 35.0, 29.5, 28.1, 32.0, 28.2, 29.4, 12.9, 18.4, and 15.7%, respectively, which were significantly correlated with HAM gene-dosage (r = 0.81, p < 0.01). Amylose content, number of elongated starch granules, and conclusion gelatinization temperature increased with the increase in HAM gene-dosage. X-ray diffraction study showed that the relative crystallinity (%) of starch granules decreased with the increase in HAM gene-dosage. The results suggested that the HAM gene-dosage was responsible for changes in starch molecular structure and organization of starch granules and, in turn, the RS formation in the maize ae mutant starch.