Great progress has been made in the integration of Unmanned Aerial Vehicle (UAV) magnetic measurement systems, but the interpretation of UAV magnetic data is facing serious challenges. This paper presents a complete workflow for the detection of the subsurface objects, like Unexploded Ordnance (UXO), by the UAV-borne magnetic survey. The elimination of interference field generated by the drone and an improved Euler deconvolution are emphasized. The quality of UAV magnetic data is limited by the UAV interference field. A compensation method based on the signal correlation is proposed to remove the UAV interference field, which lays the foundation for the subsequent interpretation of UAV magnetic data. An improved Euler deconvolution is developed to estimate the location of underground targets automatically, which is the combination of YOLOv3 (You Only Look Once version 3) and Euler deconvolution. YOLOv3 is a deep convolutional neural network (DCNN)-based image and video detector and it is applied in the context of magnetic survey for the first time, replacing the traditional sliding window. The improved algorithm is more satisfactory for the large-scale UAV-borne magnetic survey because of the simpler and faster workflow, compared with the traditional sliding window (SW)-based Euler method. The field test is conducted and the experimental results show that all procedures in the designed routine is reasonable and effective. The UAV interference field is suppressed significantly with root mean square error 0.5391 nT and the improved Euler deconvolution outperforms the SW Euler deconvolution in terms of positioning accuracy and reducing false targets.