The invention discloses a design method for two-level precodes of a cognitive MIMO communication system and relates to the technical field of the cognitive MIMO communication systems. In the MIMO communication system, a cognitive user adopts an opportunistic access mode to use space sub-channels of a main user, and interference, generated on the main user, of the cognitive user is reduced through an interference alignment method; interference alignment is achieved through precode designing of all transmitting ends of the cognitive user. According to the transmission performance of the main user, a precode matrix can be designed on the basis of transmission channel matrix singular value decomposition, and power distribution of the transmitting ends is achieved by the utilization of a water-filling method; the design for the two-level precodes is performed on the transmitting ends of the cognitive user, the first level precode is used for aligning the interference generated, on the main user, of the cognitive user to the space sub-channels available for the main user, and the second level precode is used for promoting the transmission performance of the cognitive user. By the adoption of the design method for the two-level precodes, under the condition that the interference, on the main user, of the cognitive user is reduced, the transmission performance of the cognitive user is guaranteed.