Aerial magnetic surveying serves as a critical technical approach in various fields, including mineral resource exploration, geological structure analysis, detection of abandoned oil and gas wells, and localization of underground magnetic anomalies. With the rapid advancement of Unmanned Aerial Vehicle (UAV) technology, its application has expanded significantly into the domain of aerial magnetic gradient detection. Considering the limitations of current UAV-based magnetic gradient detection systems—such as narrow magnetic field measurement ranges, substantial magnetic interference from the carrier, and pronounced low-frequency noise, which collectively hinder high-precision detection—this study proposes a quadrotor UAV-based vertical magnetic gradient detection system capable of effectively acquiring vertical magnetic gradient data. The system establishes an airborne magnetic measurement platform by integrating a quadrotor UAV with a Bartington Mag-03 fluxgate magnetometer and a data acquisition system. A specially designed variable vertical linkage structure enables the magnetometer to be vertically mounted 6 meters beneath the UAV. During flights under wind conditions of level 4 or lower, the magnetometer remains sTable and vertically oriented, with magnetic interference from the UAV motors being negligible. To address the challenge of magnetic compensation under higher wind conditions, which necessitates shortening the connecting rod, field experiments were conducted, including UAV magnetic interference tests and pipeline detection trials. The collected magnetic data were processed and analyzed to implement magnetic interference compensation. The experimental results demonstrate that all system performance indicators meet the technical specifications required for aeromagnetic surveys, enabling safe, efficient, and high-quality vertical magnetic gradient detection. The issues of magnetometer instability and magnetic interference compensation difficulties have been effectively resolved, resulting in significantly improved magnetic measurement data quality. This system provides advanced technical support for China's aerial vertical magnetic gradient detection capabilities and holds great promise for future applications.