The invention mainly relates to the field of cultivation and discloses a cotton breeding matrix. The cotton breeding matrix is prepared from cotton straws, corn stalks, wheat straws, biogas residues, sweet potato residues, Potamogeton crispus, cow dung, edible fungus wastes, EM bacteria, traditional Chinese medicines, clonidine, rose flower extract, river sand, vermiculite and medical stone. The cotton breeding matrix is prepared from abundant raw materials, has balanced nutrition, can provide the necessary nutrients for cotton growth, has antibacterial and insecticidal effects, enhances the disease resistance of cotton, and realizes an emergence rate of cotton of 89%, a survival rate of 94%, a disease and pest rate of 4% and economic efficiency of 9.6%. Cotton straw as a raw material is fully used and application approaches of clonidine and rose flower extract are increased. Through strain culture fermentation and use of medical stone rich in small molecule beneficial ingredients, the growth of cotton is promoted, a planting period is shortened by 15 to 20 days and planting efficiency is accelerated. Through cooperation of medical stone and a variety of Chinese herbal medicines, the cotton breeding matrix inhibits occurrence of pests and diseases, reduces an incidence rate of pests and diseases and saves a planting cost.