Microplastics in natural aquatic environments have caused major environmental crises due to their resistance to biodegradation and ingestion toxicity. Conventional cleaning methods, such as tow nets and propeller-based suction pumps, are inadequate due to their limited maneuverability and high levels of biological intrusion. In this study, we present a multifunctional bio-inspired robotic module, inspired by the efficient filter-feeding mechanism of the Giant Larvacean, for active particle-laden fluid suction. The design is fundamentally based on the fluid–structure interaction of a flexible undulating structure, employing non-uniform stiffness distribution and a tailored actuation scheme to optimize the trade-off between suction and propulsion. We analyze single-module performance at various actuation frequencies, with particular attention to the effect of the ratio between the natural frequency and the input frequency on pumping and propulsion, and identified optimal motions based on considerations of efficiency, stability, and environmental compatibility. Furthermore, we designed the robot structure based on the Giant Larvacean mechanism, and proposed a FastPID algorithm to reduce the tuning time required in systems that do not demand high-precision control. Lastly, we demonstrate the feasibility, adaptability, and maneuverability of multimodule assemblies. This flexible bio-inspired robotic module opens up a novel pathway toward low-impact microplastic remediation with the potential for large-scale field deployment.