In order to ensure the reliability of navigation and positioning systems in China's airborne geophysical work, research has been conducted on the Beidou-3 navigation satellite system to ensure high-quality and efficient completion of aerogeophysical work, and to enhance the country's independence and safety in the field of aerogeophysical exploration. Firstly, research was conducted on the Beidou-3 navigation satellite system, designing its positioning and signal acquisition modules and converting the collected data into formats. The developed system was statically tested in Shijiazhuang and Zhongwei, and the test results showed that the convergence time of the Beidou-3 navigation satellite system developed in this paper was 21 minutes, with a static positioning accuracy of 0.061 m, which can well meet the requirements of aerogeophysical survey. Further testing and application of the system were conducted in the Ordos measurement area. The developed Beidou-3 positioning system and GPS system were loaded onto the P-750 aircraft, and completed data collection for 1686 kilometers of survey line. The average difference in positioning error between the two positioning systems was 0.002 m, and the number of measrement lines with Beidou-3 positioning accuracy higher than GPS positioning accuracy accounted for 40%. After track recovery, the airborne/magnetic data collected by GPS and Beidou systems at different measurement times were compared. The results showed that there was no mutual interference between the developed Beidou positioning system and GPS system, and they could work independently of each other. This indicates that the developed Beidou positioning system can effectively complete aerogeophysical survey, with high reference and application value, providing new means and methods for positioning of aerogeophysical survey, and improving the security of exploration information.