Accurately determining microdroplet size and uniformity in dispersed phase systems is key for assessing emulsion stability, and essential for quality monitoring and control of emulsion products. Microscopic imaging probes have provided intuitive and advanced insights for characterizing particle microscopic morphology and dispersion in multiphase flows. However, wide size distributions, edge-cutting, overlapping, and high-density target droplets can compromise the image processing accuracy, thereby affecting the precise assessment of emulsion status. In this study, we present a deep learning-based intelligent workflow for microdroplet characterization using an in-situ high-speed particle imaging probe combined with advanced image processing techniques. With the assistance of progressive automatic annotation, a droplet image database was constructed for training the Mask R-CNN model. By incorporating image patching and supervised data augmentation strategies, our well-trained model with accuracy of 95.5% can precisely detect, localize, and segment microscale droplets with various patterns. Additionally, the shape reconstruction module visualizes true shapes of overlapping and edge-cutting droplets, facilitating precise quantification of droplet size information. To validate the feasibility and generalizability of the proposed workflow, we obtained sufficient droplet images through offline sampling during emulsion processes while employing back and front illumination for in-situ monitoring. The automated method achieves precise droplet detection and size measurement, demonstrating its immense potential in online monitoring, evaluation, and control of emulsion quality.