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Microplastics (MPs) are prevalent in aquatic environments and pose a serious risk to human health through the adsorption of toxic substances and entry into the food chain. Therefore, the development of effective removal strategies is essential. Mini-hydrocyclones (MHCs) offer a promising solution for MP separation owing to their high throughput, rapid processing, and low maintenance. However, their performance diminishes when interacting with MPs with densities similar to that of water. To overcome this problem, microbubbles (MBs) have been introduced to reduce the apparent density of MPs and improve their separation efficiency. Nevertheless, the interactions between MPs and MBs within the complex flow of MHCs remain poorly understood, highlighting the need for further investigation and optimization. This study examined the MP separation performance of an MHC under varying flow rates, MB concentrations, and surface charge conditions. High-speed visualization revealed strong MB–MP attachment, even within the short residence time of the MHC, and confirmed that the air core plays a central role in the separation dynamics. Under optimal conditions (300 mL/min and 55,500 MBs/mL), the MP separation efficiency improved by up to 34% compared to tests without MBs. Conversely, excessive MB concentrations or low flow rates led to unstable or oversized air cores, disrupting the internal flow and reducing the efficiency. Moreover, the system successfully achieved density-based separation of mixed high- and low-density MPs through MB-assisted underflow and overflow collection. These findings advance our understanding of MB-assisted separation mechanisms and help define practical operating conditions. These results demonstrate the potential of the MHC system as a compact and scalable solution for decentralized water treatment applications.