<p>Multilayer microcapsules containing a small particle within a larger capsule have recently attracted considerable attention owing to their potential applications in diverse fields, including drug delivery, active ingredient storage, and chemical reactions. These complex capsules have been fabricated using interfacial polymerization or seeded emulsion polymerization. However, these methods often require complex and lengthy polymerization processes, limiting their utility, particularly in biopolymer systems. This study introduces a simple and efficient approach for preparing rattle-shaped cellulose acetate (CA) microcapsules through sequential phase separation in droplets. We systematically examine the effects of various preparation parameters, including the amount of co-solvent, initial droplet size, and flow rates, and reveal that the incorporation of a co-solvent—ethyl acetate (EA)— in the dispersed phase significantly impacts the microcapsule morphology. Our findings demonstrate a transition from a core-shell to a rattle-shaped structure as the EA concentration increases. Furthermore, the initial droplet diameter and flow rates influence microcapsule formation—larger droplets and reduced continuous-phase flow rates favor the development of multi-layered structures. These results indicate that the formation mechanism of these rattle-shaped microcapsules arises from the establishment of a radial solvent concentration gradient and subsequent phase separation within the droplets, driven by kinetic rather than thermodynamic factors.</p>