A method for fabricating 3D microstructure is disclosed. A matching fluid is arranged between the mask and the photoresist layer. When the mask and photoresist layer perform the relative scanning and exposure process simultaneously, the matching fluid will reduce the diffraction error, so that the gap between the mask and the photoresist layer becomes more tolerable. Besides, the matching fluid also acts as a lubricant for achieving a smooth scanning process, so as to fabricate a high-precision large-area 3D optical microstructure.