Objective: To explore the differences in clinical characteristics and interocular interactions between patients with anisometropic amblyopia and ametropic amblyopia. Methods: Cross-sectional study. The newly diagnosed anisometropic (the binocular difference in spherical equivalent≥1.00 D) amblyopia patients and ametropic amblyopia patients (aged 4 to 6 years) in Beijing Tongren Hospital from January 2020 to December 2022 were involved. Patients were further categorized by the refractive status after cycloplegia, including hyperopia, myopia, astigmatism, hyperopia with astigmatism, myopia with astigmatism, mild anisometropia and severe anisometropia. Quantitative measurements of best-corrected visual acuity (logMAR), stereoacuity (transformed to log units), perceptual eye position and interocular suppression were performed, and the differences between groups were analyzed. The rank sum test was used for statistical evaluation. Results: The average age of 45 ametropic amblyopia patients (21 males and 24 females) and 84 anisometropic amblyopia patients (48 males and 36 females) was 5.0 (4.0, 5.0) years and 5.0 (4.0, 6.0) years, respectively. The interocular differences in spherical equivalent [2.56 (1.50, 4.19) D vs. 0.25 (0.13, 0.56) D] and best-corrected visual acuity [0.40 (0.18, 0.70) logMAR vs. 0.07 (0.00, 0.12) logMAR] were larger in patients with anisometropic amblyopia than those with ametropic amblyopia. The anisometropic amblyopia patients had worse stereoacuity [2.60 (2.00, 2.90) log arcsec vs. 2.00 (2.00, 2.30) log arcsec] and deeper suppression [20.0% (13.3%, 40.0%) vs. 10.0% (0, 23.3%)], compared with the ametropic amblyopia patients. The differences were all statistically significant (P<0.05). The suppression and stereoacuity between patients with hyperopic anisometropic amblyopia [suppression, 30.0% (17.5%, 50.0%); stereoacuity, 2.90 (2.30, 2.90) log arcsec] and astigmatic anisometropic amblyopia [suppression, 10.0% (0, 20.0%); stereoacuity, 2.00 (2.00, 2.30) log arcsec] were significantly different (P<0.05). The differences of suppression and stereoacuity between patients with severe (binocular difference in spherical equivalent>2.50 D) [suppression, 30.0% (20.0%, 53.3%); stereoacuity, 2.90 (2.57, 2.90) log arcsec] and mild anisometropia [suppression, 20.0% (0, 30.0%); stereoacuity, 2.00 (2.00, 2.90) log arcsec] were also statistically significant (P<0.05). Conclusions: Patients with anisometropic amblyopia have deeper binocular suppression, worse stereoacuity and more severe binocular interaction abnormality than those with ametropic amblyopia. The severity of anisometropia affects the degree of the interaction abnormality.