Abstract: This study investigated the effect of fish oil microcapsule incorporation on the sensory characteristics, cooking performance, and flavor profile of coconut-dried shrimp composite dough. Formulations containing microencapsulated fish oil were compared with those incorporating unencapsulated oil to evaluate the functional benefits of microencapsulation. The dough samples were analyzed using a texture analyzer, rheometer, and low-field nuclear magnetic resonance (LF-NMR) to assess texture, viscoelastic behavior, and water mobility, respectively. Flavor attributes were characterized through electronic nose analysis and gas chromatography-ion mobility spectrometry (GC–IMS). Results demonstrated that the addition of 10% fish oil microcapsules to dough containing 5% coconut-dried shrimp achieved the highest overall sensory score (83.20) and exhibited a desirable yellow hue consistent with consumer preferences. Compared with both the control and unencapsulated fish oil groups, microcapsule-enriched doughs showed lower noodle breakage and cooking loss, alongside increased cooking time and water absorption. Textural analysis revealed enhanced hardness and chewiness, with reduced resilience, while rheological data confirmed a significant improvement in viscoelastic properties. GC–IMS analysis identified esters as the dominant volatile compounds contributing to the characteristic flavor profile. Collectively, these findings demonstrate that microencapsulation of fish oil effectively enhances the physicochemical and sensory quality of coconut-dried shrimp composite dough, providing a promising approach for developing omega-3-fortified staple foods with improved palatability and functionality.