A temperature-controlled microfluidic approach was developed for fabricating monodispersed agar beads with the potential to be a brand-new strategy for cultivating Cordyceps militaris. The proposed microfluidic system features a circulating water bath with precise temperature control (temperature deviation T<0.1 degrees C). This device holds the promise of allowing us to develop a temperature-controlled system, characterized as simple, low cost, and easy to set up and use. The size-controllable agar beads were achieved by utilizing microfluidic emulsification in the cross-junction channel under temperature-controlled conditions. The flow conditions of the dispersed/continuous phases were adjusted to generate various sizes of agar beads. Our results show that the microparticles produced are as small as 176 mu m with a 95% particle size distribution within 5 mu m. The prepared agar microparticles performed well as a substrate for the cultivation of C. militaris. The proposed method could also be applied for encapsulating biomaterials, enzymes, drugs, catalysts, and nanoparticles into agar beads for biomedical applications.