To promote the application of Beidou navigation satellite system (BDS) airborne equipment on civil aircraft will be faced with compatibility analysis with other loaded equipment. Iridium system has been integrated and applied in the main aircraft types of Boeing and Airbus to provide aeronautical mobile satellite (rote) services [AMS(R)S] for aircraft. The user link of iridium system overlaps with the uplink spectrum of radio determination satellite service (RDSS), and therefore the compatibility between BDS RDSS airborne equipment and iridium airborne earth station (AES) is evaluated. The isolation between airborne antennas is one of the main parameters to evaluate the electromagnetic compatibility (EMC) of airborne system. The aircraft fuselage is idealized as a smooth cylindrical surface of pure metal. By adjusting the relative position between the two antennas, the effect of antenna layout on antenna isolation is analyzed. Meanwhile, the axial ratio of receiving and transmitting antennas and the RDSS transmitting power also have an important impact on the compatibility of the two systems. The simulation results show that BDS RDSS airborne equipment will cause harmful interference to the AES of iridium system, and reasonable installation suggestions are given, which can provide a reference for the airworthiness installation of BDS RDSS airborne equipment in civil aviation.