Agricultural pests and diseases critically impact the quality and yield of crops, thereby underscoring the practical importance of their automatic monitoring, identification, and timely management in agricultural production. This study develops a targeted detection model using a deep learning approach, specifically by enhancing the Faster R-CNN algorithm. Modifications were implemented in three key areas of the basic Faster R-CNN: First, the DIOU-NMS technique was employed to optimize the ancillary network during the feature extraction phase. Secondly, an attention mechanism along with an SE module was integrated within the DIOU-NMS to augment the network’s capability. During the training phase, optimization was facilitated through stochastic gradient descent. The efficacy of the refined Faster RCNN model was established via ablation studies, and its performance was benchmarked against existing methodologies for small and general target detection. Results indicate that the enhanced Faster R-CNN framework surpasses conventional small target and generic detection models in accuracy, achieving a 6.4% higher detection rate for various pest categories compared to its predecessor. The findings affirm the potential of the advanced Faster R-CNN in effective agricultural pest detection. Furthermore, this paper advocates a tripartite strategy for pest management, encompassing phytosanitary measures, agricultural interventions, and chemical controls.