Crystallization is important to the pharmaceutical, the chemical, and the materials fields, where the morphology of crystals is one of the key factors affecting the quality of crystallization. High-throughput screening based on microfluidic droplets is a potent technique to accelerate the discovery and development of new crystal morphologies with active pharmaceutical ingredients. However, massive crystal morphologies' datum needs to be identified completely and accurately, which is time-consuming and labor-intensive. Therefore, effective morphologies' detection and small-target tracking are essential for high-efficiency experiments. In this paper, a new improved algorithm YOLOv8 (YOLO-PBESW) for detecting indomethacin crystals with different morphologies is proposed. We enhanced its capability in detecting small targets through the integration of a high-resolution feature layer P2, and the adoption of a BiFPN structure. Additionally, in this paper, adding the EMA mechanism before the P2 detection head was implemented to improve network attention towards global features. Furthermore, we utilized SimSPPF to replace SPPF to mitigate computational costs and reduce inference time. Lastly, the CIoU loss function was substituted with WIoUv3 to improve detection performance. The experimental findings indicate that the enhanced YOLOv8 model attained advancements, achieving AP metrics of 93.3%, 77.6%, 80.2%, and 99.5% for crystal wire, crystal rod, crystal sheet, and jelly-like phases, respectively. The model also achieved a precision of 85.2%, a recall of 83.8%, and an F1 score of 84.5%, with a mAP of 87.6%. In terms of computational efficiency, the model's dimensions and operational efficiency are reported as 5.46 MB, and it took 12.89 ms to process each image with a speed of 77.52 FPS. Compared with state-of-the-art lightweight small object detection models such as the FFCA-YOLO series, our proposed YOLO-PBESW model achieved improvements in detecting indomethacin crystal morphologies, particularly for crystal sheets and crystal rods. The model demonstrated AP values that exceeded L-FFCA-YOLO by 7.4% for crystal sheets and 3.9% for crystal rods, while also delivering a superior F1-score. Furthermore, YOLO-PBESW maintained a lower computational complexity, with parameters of only 11.8 GFLOPs and 2.65 M, and achieved a higher FPS. These outcomes collectively demonstrate that our method achieved a balance between precision and computational speed.