Autonomous orbit determination is the ability of navigation satellites to estimate the orbit parameters on-board using inter-satellite link (ISL) measurements. This study mainly focuses on data processing of the ISL measurements as a new measurement type and its application on the centralized autonomous orbit determination of the new-generation Beidou navigation satellite system satellites for the first time. The ISL measurements are dual one-way measurements that follow a time division multiple access (TDMA) structure. The ranging error of the ISL measurements is less than 0.25 ns. This paper proposes a derivation approach to the satellite clock offsets and the geometric distances from TDMA dual one-way measurements without a loss of accuracy. The derived clock offsets are used for time synchronization, and the derived geometry distances are used for autonomous orbit determination. The clock offsets from the ISL measurements are consistent with the L-band two-way satellite, and time–frequency transfer clock measurements and the detrended residuals vary within 0.5 ns. The centralized autonomous orbit determination is conducted in a batch mode on a ground-capable server for the feasibility study. Constant hardware delays are present in the geometric distances and become the largest source of error in the autonomous orbit determination. Therefore, the hardware delays are estimated simultaneously with the satellite orbits. To avoid uncertainties in the constellation orientation, a ground anchor station that “observes” the satellites with on-board ISL payloads is introduced into the orbit determination. The root-mean-square values of orbit determination residuals are within 10.0 cm, and the standard deviation of the estimated ISL hardware delays is within 0.2 ns. The accuracy of the autonomous orbits is evaluated by analysis of overlap comparison and the satellite laser ranging (SLR) residuals and is compared with the accuracy of the L-band orbits. The results indicate that the radial overlap differences between the ...