We enrolled 500 highly myopic eyes and 50 controls in this hospital-based prospective cohort study. The fixation ellipse angle and area in terms of the bivariate contour ellipse area (BCEA) were measured with Macular Integrity Assessment microperimetry. Optic disc tilt and rotation were evaluated with retinal images. The associations between fixation and optic disc changes were assessed. Both 63% and 95% BCEA correlated positively with axial length (AL) (both r = 0.230, P = 0.001) in highly myopic group, and were significantly higher than the control group (both P < 0.001). The direction of fixation ellipse presented clockwise rotation in the right eyes and anti-clockwise rotation in the left eyes with the increase of AL in highly myopic group (AL ≥30 vs <30 mm: OD 76.12 ± 51.17°: vs 90.60° ± 51.28°, P = 0.029; OS 94.73 ± 57.45° vs 87.82 ± 55.15°, P = 0.371). The angle between the long axis of the fixation ellipse and the long axis of the optic disc (AngleF-D) distributed in various directions: 0-30° (34.6% almost parallel) ≈60-90° (34.4% almost vertical) >30-60° (31% oblique). AngleF-D increased slightly with the AL (r = 0.105, P = 0.024). In highly myopic eyes, fixation stability decreased with the AL, and superior rotation of the fixation ellipse increased with AL. The long axis of fixation ellipse and the long axis of optic disc became less parallel to each other with increasing AL. Our data may provide clues for improvement of fixation evaluation designs of biometric instruments.