Multiphase microfluidics has attracted significant interest in making micro- and nanostructures for various applications because of its capabilities in precisely controlling and manipulating a small volume of liquids. In this review, we introduce the recent advances in making micro- and nanostructures for pharmaceutical applications, including microparticles and microcapsules for controlled release, nanoparticles for drug delivery and microgels for 3D cell culture. With the development of more advanced microfluidic systems, the research focus in this field has shifted from making simple micro- and nanostructures to multifunctional systems to achieve more desirable functions. However, these multifunctions may lose their advantages that have been demonstrated in vitro once they are applied in vivo or later in human. The key challenge is a lack of fundamental understanding of the interactions between the micro- and nanomaterials and the biology systems. Consequently, the translation of these advanced materials lags far behind their extensive laboratory research. To better understand the micro- or nano-bio interactions, the development of new in vivo-mimicking models is imperative. Microfluidics has demonstrated its great potential in creating physiologically relevant models including 3D cell culture, tumor-on-a-chip and organs-on-a-chip. Therefore, efforts towards developing 3D cell culture and biomimetic chips including tumor-on-a-chip and organs-on-chips for faster and reliable evaluation of these micro- and nanosystems are also highlighted.