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The excessive exploitation of rare earth elements (REEs) has caused major losses of non-renewable resources and damage to the ecosystem. The processes of mining and smelting produce massive amounts of wastewater with low concentrations of REEs. Consequently, the enrichment and recovery of low-concentration REEs from wastewater has significant economic and environmental value. For this purpose, operation under large phase ratios (the flow rate ratio between the aqueous phase and extractant) is more desirable and economically viable. However, the traditional REE extraction process suffers from the uneven dispersion of the extractant and the difficulty of phase separation, which leads to long extraction times and large consumption of extractants. Hence, there is an urgent need to develop a green and efficient technique to extract low concentrations of REEs from wastewater. In this work, a droplet-based microfluidic technique was used to continuously extract and recover low-concentration REEs at large phase ratios. Snowman-shaped magnetic Janus nanoparticles were added to the continuous phase as emulsifiers to facilitate uniform extractant dispersion and rapid phase separation. Several key factors affecting the extraction efficiency, including pH, residence time, and the amount of added Janus nanoparticles, were systematically investigated. Compared to batch extraction, droplet-based microfluidic extraction with the addition of Janus nanoparticles showed the advantages of a large specific surface area and fast phase separation during extraction. Meanwhile, the Janus nanoparticles exhibited good emulsification performance after three extraction cycles. In summary, the Janus nanoparticle-stabilized droplet generated by microfluidic methods provides a feasible path for the efficient enrichment and recovery of low-concentration REEs.