Collecting crop growth data in field environments is crucial for breeding research. The team’s current autonomous soybean phenotyping system requires manual control to start and stop data collection. To address the aforementioned issues, this study innovatively proposes an elliptical calibration rotating geofencing technique. Preprocess coordinates using Z-scores and mean fitting perform global error calibration via weighted least squares, calculate the inclination angle between the row direction and the relative standard direction by fitting a straight line to the same row of data, and establish a rotation model based on geometric feature alignment. Results show that the system achieves an average response time of 0.115 s for geofence entry, with perfect accuracy and Recall rates of 1, meeting the requirements for starting and stopping geographic fencing in soybean ridge trial plots. This technology provides the critical theoretical foundation for enabling a dynamic, on-demand automatic start–stop functionality in smart data collection devices for soybean field trial zones within precision agriculture.