Accurate estimation of the effective operational area of automatic transplanters is essential for evaluating machinery productivity, improving field management efficiency, and supporting digital agricultural applications. However, operational-area estimation based on low-cost BeiDou trajectories remains challenging because raw trajectories are often affected by positioning uncertainty, trajectory discontinuities, and non-productive machine movements, including headland turning, road transportation, empty transfer, and seedling loading/unloading operations. Directly using all recorded trajectories may therefore introduce considerable area overestimation, whereas excessive trajectory filtering may remove valid productive operations. This study proposes a state-aware hierarchical trajectory fusion framework coupled with a low-cost BeiDou-based monitoring system for automatic operation-state recognition and operational-area estimation of transplanters. Unlike conventional trajectory-processing approaches that mainly focus on geometric smoothing or spatial clustering, the proposed framework jointly considers positioning reliability, motion consistency, spatiotemporal continuity, and operational semantics to extract productive transplanting trajectories from noisy GNSS observations. Three field datasets containing more than 49,000 trajectory points (approximately 30,000 valid records after preprocessing) were collected from automatic transplanters operating in Xinjiang, China. The proposed framework integrated adaptive trajectory filtering, motion-consistency screening, spatiotemporal continuity optimization, and operation-state recognition to classify five operation states, including field transplanting, headland turning, empty transfer, road travel, and seedling loading/unloading. After productive transplanting trajectories were identified, coordinate transformation was applied to convert the retained trajectories into a local coordinate system for operational-area estimation using the effective working width of 1.2 m obtained from overlap and pass-spacing correction of the nominal 1.4 m width. The estimated operational areas were validated against RTK-derived reference measurements. Across the three datasets, the proposed framework achieved F1-scores ranging from 0.94 to 0.95, trajectory continuity rates of 94.2–96.5%, and effective trajectory-length retention above 99.5%. The estimated operational-area bias was limited to 0.9–1.5%, compared with 12.8–18.4% obtained from direct calculation using raw trajectories. These results demonstrate that integrating motion consistency, spatiotemporal continuity, and operational-state recognition can effectively reduce operational-area overestimation caused by non-productive trajectories. The proposed framework provides a low-cost and interpretable approach for agricultural machinery operational monitoring and operational-area estimation. Although low-cost GNSS positioning alone cannot satisfy centimeter-level autonomous navigation requirements, the proposed approach provides a practical foundation for future integration with multi-sensor perception, edge-intelligent processing, and digital agricultural management systems.