Soil salinization in Xinjiang cotton planting areas is serious. In order to utilize saline-alkali land for high cotton-yield and the sustainable development of agriculture，a pot-experiment was conducted with saline-alkali soil in Korla，southern Xinjiang，to analyze the effects of self-made natural-synthetic copolymer amendment on the germination rate，germination potential，germination index of cotton seed，the root and stem length，dry and fresh weight of cotton seedlings. The microstructure of saline-alkali soil under the action of soil amendment was also characterized by fourier transform infrared spectroscopy and scanning electronic microscopy. The results showed that the germination and early growth of cotton seeds were improved by self-made amendment 1#(mineral source potassium humate-polyacrylic acid graft salt alkali soil improver) in three different concentrations，A2 treatment (880 g soil amendent 1#+1000 mL distilled water) had the best effect，compared with CK treatment (1000 mL distilled water)，the germination potential and germination rate increased by 63.2% and 50.0%，the fresh weight and dry weight of seedlings increased by 99.0% and 76.9%，respectively. The germination seed ratio and seedling biomass were improved by self-made amendment 2#(mineral source potassium humate-polyacrylic acid blended salt alkali soil improver)under low concentration，but were suppressed under medium and high concentration. The infrared spectrum of the soil with self-made amendment had little change，and the absorption peak of organic matter was slightly increased. Adding soil amendment could improve the dense and compact structure of the original soil，cause aggregation between soil particles and roughening of the soil surface，the A2 treatment soil with self-made amendment 1# had the largest agglomerated particles and the largest intergranular pores，the soil treated with self-made amendment 2# had also become loose，but there was little change between different concentrations.