Polymer particles are key materials in various biomedical applications, including drug delivery, cellular immunity, cell capture, biochip, etc. Droplets produced by microfluidics have been widely applied as templates for the fabrication of polymer particles with controllable sizes and narrow size distributions. Compared to smooth polymer particles, those with surface microstructures (e.g., tentacles, bubbles, wrinkles and pits) are more attractive due to their increased surface area and biomimetic structural characteristics. In this review, we summarized representative methods for the preparation of monodispersed polymer particles with various surface microstructures based on droplet microfluidics, as well as their typical bioapplications in drug delivery, cellular immunity and cell capture. Finally, the current challenges and further development in this research area are discussed.