Microfluidic magnetophoresis is an effective technique to separate magnetically labeled bioconjugates in lab-on-a-chip applications. However, it is challenging and expensive to fabricate and integrate microscale permanent magnets into microfluidic devices with conventional methods that use thin-film deposition and lithography. Here, we propose and demonstrate a simple and low-cost technique to fabricate microscale permanent magnetic microstructures and integrate them into microfluidic devices. In this method, microstructure channels were fabricated next to a microfluidic channel and were injected with a liquid mixture of neodymium (NdFeB) powders and polydimethylsiloxane (PDMS). After the mixture was cured, the resulted solid NdFeB–PDMS microstructure was permanently magnetized to form microscale magnets. The microscale magnets generate strong magnetic forces capable of separating magnetic particles in microfluidic channels. Systematic experiments and numerical simulations were conducted to study the geometric effects of the microscale magnets. It was found that rectangular microscale magnets generate larger (H· ∇) H which is proportional to magnetic force and have a wider range of influence than the semicircle or triangle magnets. For multiple connected rectangular microscale magnet, additional geometric parameters, including separation distance, height and width of the individual elements, further influence the particle separation and were characterized experimentally. With an optimal size combination, complete separation of yeast cells and magnetic microparticles of similar sizes (4µm) was demonstrated with the multi-rectangular magnet microfluidic device.