Multicore millimeter-sized calcium alginate capsules are promising carriers for bioactive substances. In this work, a monoaxial suspension electrospraying-internal gelation technique to prepare multicore millimeter-sized fish oil-calcium alginate capsules with homogenous calcium alginate gel structure. The obtained internal gelation-based capsules showed similar fish oil contents (7.9% ± 1.0%–8.7% ± 0.5%) and increased alginate salts (20.9%–33.1%) with the increase of calcium carbonate concentrations (1, 2, 3, 4, 5, and 6 g/L). Internal gelation could significantly inhibit the dehydration and fish oil leakage than external gelation for the fish oil-loaded calcium alginate capsules. The obtained internal gelation-based capsules had better mask ability on the surface flavors than external gelation-based capsules. The obtained internal gelation-based capsules had good potentials for specific and sustained release of fish oil into the small intestines of human being. All these results suggested the obtained capsules were promising for the research and development of functional foods and drugs. This work also provided a simple, cost-effective, and efficient approach to prepare multicore millimeter capsules with homogeneous calcium alginate gel structure.