The invention discloses a structure and application of an Enterovirus 71 (EV71) 3C protease and belongs to the field of RNA virus protein. The invention also discloses an application of the 3C protease and a substrate binding groove thereof in drug design. The protein provided by the invention has a special substrate binding groove and new EV71 virus 3C protease drugs are designed according to the spatial structure of the substrate binding groove, thus the inhibitors aiming at the EV71 virus 3C protease, which are more specific and have better effect, can be obtained, potential drug candidates can be provided for the clinical treatment of hand, foot and mouth disease and the EV71 virus 3C protease has very high application value.