Inter-satellite link (ISL) plays an essential role in current and future Global Navigation Satellite System (GNSS). In this study, we investigate the impact of ISL observations on precise orbit determination for BeiDou-3 Navigation Satellite System (BDS-3) Medium Earth Orbit (MEO) satellites based on different Extended CODE Orbit Models (ECOM). Thanks to the better observation geometry of the Ka-band ISL data compared to the L-band data for BDS-3 MEO satellites, the ISL solution substantially reduces Orbit Boundary Discontinuity (OBD) errors, except for C30, which suffers from unstable Ka-band hardware delay. From the external quality analysis, ISL significantly enhances the reliability of the orbit of MEO satellites manufactured by the China Academy of Space Technology (CAST). The standard deviation (STD) of the satellite laser ranging (SLR) residuals is approximately 2.5 cm, and the root mean square (RMS) is reduced by 10–23% compared to L-band solutions. Besides, the Sun-elongation angle dependent systematic error in SLR residuals nearly vanishes based on the reduced 5-parameter ECOM (ECOM1) or extended 7-parameter ECOM (ECOM2) with ISL data. This is because the ISL reduces the correlation between state parameters and solar radiation pressure (SRP) parameters as well as those among SRP parameters, leading to a more accurate estimation of both orbit and SRP perturbations, particularly those along B direction. This confirms that the deficiency of the SRP models for BDS-3 CAST satellites can be compensated by using better observation geometry from ISL data. On the other hand, for the satellite manufactured by Shanghai Engineering Center for Microsatellites (SECM), the ISL allows for a more accurate estimation of the Bc1 parameter in the ECOM1 model. This only reduces linear systematic error, possibly because the impact generated by the satellite bus cannot be entirely absorbed by the B-direction parameters.