Positioning of spacecraft (e.g., geostationary orbit (GEO), high elliptical orbit (HEO), and lunar trajectory) is crucial for mission completion. Instead of using ground control systems, global navigation satellite system (GNSS) can be an effective approach to provide positioning, navigation and timing service for spacecraft. In 2020, China finished the construction of the third generation of BeiDou navigation satellite system (BDS-3); this global coverage system will contribute better sidelobe signal visibility for spacecraft. Meanwhile, with more than 100 GNSS satellites, multi-GNSS navigation performance on the spacecraft is worth studying. In this paper, instead of using signal-in-space ranging errors, we simulate pseudorange observations with measurement noises varying with received signal powers. Navigation performances of BDS-3 and its combinations with other systems were conducted. Results showed that, owing to GEO and inclined geosynchronous orbit (IGSO) satellites, all three types (GEO, HEO, and lunar trajectory) of spacecraft received more signals from BDS-3 than from other navigation systems. Single point positioning (SPP) accuracy of the GEO and HEO spacecraft was 17.7 and 23.1 m, respectively, with BDS-3 data alone. Including the other three systems, i.e., GPS, Galileo, and GLONASS, improved the SPP accuracy by 36.2% and 19.9% for GEO and HEO, respectively. Navigation performance of the lunar probe was significantly improved when receiver sensitivity increased from 20 dB-Hz to 15 dB-Hz. Only dual- (BDS-3/GPS) or multi-GNSS (BDS-3, GPS, Galileo, GLONASS) could provide continuous navigation solutions with a receiver threshold of 15 dB-Hz.