The invention provides a genetic intelligent seed breeding and production system for crossbreeding and production of crops and application thereof. The system contains a GAT system vector, and the vector comprises five functional element expression cassettes: a plant male fertility restoration gene element expression cassette used for restoring male fertility of recessive genic male sterility mutants, a plant pollen abortion gene element expression cassette used for removing pollen containing GAT and keeping a heterozygotic state or a hemizygotic state of a GAT maintainer line, a chemical herbicide positive selection expression cassette used for gene transformation and GAT maintainer line impurity removal and purification, a chemical herbicide negative selection expression cassette used for removing herbicide-sensitive GAT maintainer line pollen and seed escape and removing impurities and purifying a GAT sterile line, and a seed screening element expression cassette used for mechanically sorting seeds. The system can be used for crossbreeding and hybrid seed production of plant recessive genic male sterility materials, so that new varieties of plants with high quality, high yield, wide applicability and high resistance and seeds of the plants are obtained.