Abstract: To satisfy the requirements of highly autonomous and real-time Jupiter exploration, an autonomous orbit determination method based on active-reference measurements and stellar aberration is proposed. An onboard active optical reference source is used to establish a common alignment reference for multiple star trackers. By combining stellar aberration measurements derived from the optical axes of different star trackers with observations of Jupiter’s line-of-sight direction and apparent angular radius from a wide-field navigation sensor, autonomous spacecraft orbit determination is achieved. A stellar aberration measurement model and an active-reference geometric constraint model are formulated, and an Extended Kalman Filter-based estimation algorithm is developed. On-orbit experiments using a low-Earth-orbit satellite demonstrate a positioning accuracy better than 5 km, validating the feasibility of the proposed approach for high-precision autonomous navigation of deep-space spacecraft under long-range weak-signal conditions.