In this study, biochar was produced in a microwave pyrolysis reactor and three microwave reaction conditions were introduced. They were pyrolysis temperatures (500, 600, 700, 800, and 900 degrees C), microwave powers (600, 650, 700, 750, and 800 W), and pyrolysis times (30, 40, 50, 60, and 70 min), respectively. The produced biochar was mixed with deionized water and then treated with water washing in a shaker. The yields and microstructure of biochar obtained from the microwave reactor were detailed and the pore structure of washed biochar was also studied. Results showed that the corn stover biochar yield ranged between 44.71 wt.% and 59.92 wt.% depending on the conditions used. The pores in biochar were dominated by macropores and mesopores. As the three reaction conditions were elevated, nanoscale pores appeared, pores were clogged, the pore structure became more obvious and the biochar structure got fragile. Water-washing treatment enlarged the pore sizes, cleaned the clogged pores, and removed water-soluble salts. At longer pyrolysis times, the action of water flow can cause biochar to collapse This study can provide guidance for future microstructure regulation of biochar. [Graphical abstract]