Background: Given the severe economic burden that citrus greening disease imposes on fruit farmers and related industries, rapid and accurate disease detection is particularly crucial. This not only effectively curbs the spread of the disease, but also significantly reduces reliance on manual detection within extensive citrus planting areas. Objective: In response to this challenge, and to address the issues posed by resource-constrained platforms and complex backgrounds, this paper designs and proposes a novel method for the recognition and localization of citrus greening disease, named the HHS-RT-DETR model. The goal of this model is to achieve precise detection and localization of the disease while maintaining efficiency. Methods: Based on the RT-DETR-r18 model, the following improvements are made: the HS-FPN (high-level screening-feature pyramid network) is used to improve the feature fusion and feature selection part of the RT-DETR model, and the filtered feature information is merged with the high-level features by filtering out the low-level features, so as to enhance the feature selection ability and multi-level feature fusion ability of the model. In the feature fusion and feature selection sections, the HWD (hybrid wavelet-directional filter banks) downsampling operator is introduced to prevent the loss of effective information in the channel and reduce the computational complexity of the model. Through using the ShapeIoU loss function to enable the model to focus on the shape and scale of the bounding box itself, the prediction of the bounding box of the model will be more accurate. Conclusions and Results: This study has successfully developed an improved HHS-RT-DETR model which exhibits efficiency and accuracy on resource-constrained platforms and offers significant advantages for the automatic detection of citrus greening disease. Experimental results show that the improved model, when compared to the RT-DETR-r18 baseline model, has achieved significant improvements in several key performance metrics: the precision increased by 7.9%, the frame rate increased by 4 frames per second (f/s), the recall rose by 9.9%, and the average accuracy also increased by 7.5%, while the number of model parameters reduced by 0.137×107. Moreover, the improved model has demonstrated outstanding robustness in detecting occluded leaves within complex backgrounds. This provides strong technical support for the early detection and timely control of citrus greening disease. Additionally, the improved model has showcased advanced detection capabilities on the PASCAL VOC dataset. Discussions: Future research plans include expanding the dataset to encompass a broader range of citrus species and different stages of citrus greening disease. In addition, the plans involve incorporating leaf images under various lighting conditions and different weather scenarios to enhance the model’s generalization capabilities, ensuring the accurate localization and identification of citrus greening disease in diverse complex environments. Lastly, the integration of the improved model into an unmanned aerial vehicle (UAV) system is envisioned to enable the real-time, regional-level precise localization of citrus greening disease.