The invention discloses a method for planting cotton at muddy coastal heavy saline-alkali land. The method for planting the cotton at the muddy coastal heavy saline-alkali land includes steps of soil improvement, fertilizer increase, furrowing, seeding, growing period management and harvesting, wherein the other field management measures are the same with those of the normal management method. Based on salinity and soil structure features of the muddy coastal heavy saline-alkali soil, the growth rhythm of the cotton at the saline-alkali land, and the soil improvement and fertilizer increase technology, the cotton yield and quality are improved at the saline-alkali land through regulating and controlling the cotton plant height in the whole process and using the monosomic technology for controlling reasonable fruit branch numbers.