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°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 μm with a 95% particle size distribution within 5 μm. 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.