The invention discloses a high-yield cultivation method of crop rotation of sea island cottons with long and short fruit branches, which comprises the following steps of: autumn tillage and winter irrigation, fine land preparation, preparation of suitable varieties, field planting mode, scientific field management and timely harvesting; according to the method, the long fruit branch sea island cotton and the short fruit branch sea island cotton are planted in an intercropping way, so that the marginal effect of the long fruit branch sea island cotton can be increased, the utilization rate of space resources is effectively improved, and the economic benefit is greatly improved; the method mainly adopts the currently commonly used planting mode of machine-picked cotton in Xinjiang, one filmcorresponds four rows, one film of long fruit branch loose plant type sea island cotton is adjacent with two films of short fruit branch compact plant type sea island cotton and one film of long fruitbranch sea island cotton, the arrangement is repeated in this way, the arrangement of crops in the field is optimized, the planting layout of the plant type structure alternate arrangement of loose-compact-loose is integrally formed, no significant difference exists in the quality of the sea island cotton fiber, but the yield of seed cotton and lint cotton can be increased by 10.07% and 10.95% respectively, and the yield and benefit of cotton per unit area can be obviously improved.