Low abundance cell sorting has fundamental applications in cell research and therapy, such as cancer diagnosis, cell transplantation, and immunology. However, various methods for isolating low abundance cells are challenging due to the low cell recovery rate and throughput. In this paper, we propose a magnetic nanoparticle assisted microfluidic system (MNPAMS) for selecting low abundance cells with high cell recovery rate. This system integrates an active magnetic nanoparticles (MNPs)-based sorting mechanism and a passive size-based capture mechanism into one microfluidic chip. Polydimethylsiloxane (PDMS) was used to fabricate a bilayer microfluidic chip. The magnetic and fluid field models of the MNPAMS were analyzed using finite element method (FEM). Furthermore, the sorting performance was validated by mixed HeLa cell samples of three different concentrations. The experimental results show the target cells were concentrated in the arrays of structures 2 and structures 3. For different concentrations, the target cell recovery rate is relatively stable up to maximum 99.5%. Besides, the recovery efficiency of low abundance cells sorting can reach 88.6% for a 1/100 of the original sample concentration. Based on these results, the MNPAMS has the potential to facilitate liquid biopsy and fundamental biomedical studies with high target cells recovery. • A Magnetic Nanoparticle Assist Microfluidic System was proposed for cell sorting. • The system combined magnetic labeling with microstructures capturing mechanism. • The highest recovery efficiency could reach 88.6% for low abundance cell sorting.