Transforming in-situ transmission electron microscopy (TEM) imaging into a tool for spatially-resolved operando characterization of solid-state reactions requires automated, high-precision semantic segmentation of dynamically evolving features. However, traditional deep learning methods for semantic segmentation often encounter limitations due to the scarcity of labeled data, visually ambiguous features of interest, and small-object scenarios. To tackle these challenges, we introduce MultiTaskDeltaNet (MTDN), a novel deep learning architecture that creatively reconceptualizes the segmentation task as a change detection problem. By implementing a unique Siamese network with a U-Net backbone and using paired images to capture feature changes, MTDN effectively utilizes minimal data to produce high-quality segmentations. Furthermore, MTDN utilizes a multi-task learning strategy to leverage correlations between physical features of interest. In an evaluation using data from in-situ environmental TEM (ETEM) videos of filamentous carbon gasification, MTDN demonstrated a significant advantage over conventional segmentation models, particularly in accurately delineating fine structural features. Notably, MTDN achieved a 10.22% performance improvement over conventional segmentation models in predicting small and visually ambiguous physical features. This work bridges several key gaps between deep learning and practical TEM image analysis, advancing automated characterization of nanomaterials in complex experimental settings.