This study aims to assess the autonomous navigation performance of an asteroid orbiter enhanced using an inter-satellite link to a beacon satellite. Autonomous navigation includes the orbit determination of the orbiter and beacon, and asteroid gravity estimation without any ground station support. Navigation measurements were acquired using satellite-to-satellite tracking (SST) and optical observation of asteroid surface landmarks. This study presents a new orbiter-beacon SST scheme, in which the orbiter circumnavigates the asteroid in a low-altitude strongly-perturbed orbit, and the beacon remains in a high-altitude weakly-perturbed orbit. We used Asteroid 433 Eros as an example, and analyzed and designed low- and high-altitude orbits for the orbiter and beacon. The navigation measurements were precisely modeled, extended Kalman filters were devised, and observation configuration was analyzed using the Cramer-Rao lower bound (CRLB). Monte Carlo simulations were carried out to assess the effects of the orbital inclination and altitudes of the orbiter and beacon as key influencing factors. The simulation results showed that the proposed SST scheme was an effective solution for enhancing the autonomous navigation performance of the orbiter, particularly for improving the accuracy of gravity estimation.