The invention provides a method and a device for predicting permeability on the basis of pore structures of carbonate rock. According to the method, firstly, the pore structures are classified on thebasis of similarity level of mercury injection curves, then each type of pore structure reservoir is analyzed with a mathematical statistics method, key pore throat size Rs for controlling permeability is identified, and the relation between the key pore throat size Rs and the permeability of each type of pore structure is established, so that the permeability of a highly anisotropic reservoir canbe predicted. According to the provided scheme, microscale and macroscale combination is realized by comprehensively using a core, property testing, mercury injection and well logging, the theoretical basis is firm, the operability is high, and practice proves that the method and the device have good application effect and high applicability to porous-type carbonate rock reservoirs, can effectively predict the permeability of the carbonate rock and have great significance in identification of barriers and interlayers of highly anisotropic carbonate rock as well as design and regulation of oiland gas field development programs.