For the collapse and adhesion of photoresist with nano-structures due to the surface tension of deionized water in electron beam lithography, a drying method based on microwave heating is proposed to improve the quality of the photoresist with nano-structures. The method makes use of the microwave penetrate the photoresist to heat the water stored between resist patterns directly, and the water will evaporate with absorbing energy of microwave. Thus the collapse and adhesion of the photoresist with nano-structures can be avoided. The proposed method is used for drying photoresist lines with a height of 260 nm, width of 16 nm and photoresist pillars with the diameter of 20 nm in electron beam lithography and development. The results show that the lines and the array containing of 15 625 pillars are no collapse and adhesion, which demonstrates that the microwave with an alternating electric field can reduce the sizes of water clusters and the tension of deionized water dramatically.