The unmanned aerial vehicle (UAV)-towed geomagnetic surveying technique provides significant benefits in minimizing platform-induced magnetic interference, making it a highly effective approach for high-precision aeromagnetic surveys. This study introduces a novel towed geomagnetic surveying system based on a Coherent Population Trapping (CPT) atomic magnetometer, which uniquely utilizes a single-probe architecture for the first time. By harnessing the high sensitivity and omnidirectional self-sensing capabilities of the CPT atomic magnetometer, the system facilitates high-precision geomagnetic measurements across all latitudes. To validate the system′s performance, multiple flight experiments were conducted in offshore regions. A comprehensive data processing and magnetic mapping methodology was developed, incorporating key techniques such as heading error compensation, suppression of platform magnetic interference, correction of geomagnetic diurnal variations, adjustment of the geomagnetic reference field, and high-resolution interpolation-based mapping, significantly improving the accuracy and reliability of the measurements. Experimental results revealed that before data processing, the total accuracy of airborne magnetic measurements was 2.517 nT (1σ). After applying extensive error compensation and optimization, the accuracy improved markedly to 0.849 nT (1σ), effectively reducing systematic errors. Additionally, to evaluate the system′s stability under varying measurement conditions, data from two independent survey flights were processed identically and analyzed for consistency. The results showed a correlation coefficient of 99.8% between the two independently generated geomagnetic anomaly maps, with a root mean square error of 1.149 nT, confirming the system′s excellent data consistency and repeatability. These findings demonstrate that the developed CPT atomic magnetometer-based towed geomagnetic surveying system successfully addresses the challenges of platform-induced magnetic interference in conventional aeromagnetic surveys, while achieving high-precision magnetic field measurements and exceptional stability in real-world flight experiments.