In order to meet accuracy requirements of long-term almanac parameters for assisting inter-satellite link signal acquisition in autonomous navigation mode, in this paper, without changing the almanac model, we propose the scheme of different fitting arc length for different types of satellites. Considering position fitting maximum error, fitting stability and satellite storage resources on-board, the optimal fitting arc length for long-term almanac suitable for autonomous navigation is designed for Beidou geostationary earth orbit (GEO), inclined geosynchronous orbit (IGSO) and medium earth MEO navigation satellites. Based on the actual orbit data of 13 Beidou satellites in-orbit in 2013, a variety of fitting arc lengths were used to fit the almanac. The comparative analysis shows that MEO satellites still adopt 7-day fitting arc length while IGSO and GEO satellites utilize 3-day fitting arc length. The verification results show that the optimal fitting arc length scheme proposed in this paper satisfies accuracy requirements of inter-satellite link construction. Furthermore, it has good stability and engineering feasibility.