Abstract: Studies have shown low soil oxidation reduction potential, soil available nutrients contents and rice yield in cold waterlogged paddy fields due to long-term flooding in cold spring. A field experiment along with laboratory analysis was conducted to determine the effects of improving soil fertility and rice growth by application of pure chemical fertilizers, stabilized compound fertilizers, combined compound fertilizer with chicken manure, and combined compound fertilizer with composted chicken manure. The results showed that compared with pure chemical fertilizer treatment, the application of combined compound fertilizer with composted chicken manure treatment effectively increased the contribution of loose humus by 10.8% while reduced the contribution of compact humus by 15.5%. Thus organic matter content and active organic matter content of the soils increased respectively by 8.9% and 4.0%. Also soil cation exchange capacity increased by 10.2%, while soil bacterium content and microorganism activity increased respectively by 390.0% and 13.0% during early rice growth season. At the same time, the application of combined compound fertilizer with composted chicken manure increased soil aluminum phosphate salt and calcium phosphate salt contents by 40.0% and 28.0%, respectively. While percent aluminum phosphate salt and calcium phosphate salt increased, percent occluded phosphorus decreased. Soil insoluble phosphate was transformed into soluble phosphorus, and soil available phosphorus content significantly increased. As absorbed phosphorus and potassium increased respectively by 14.0% and 127.0% during early rice growth season, early and late rice yields increased respectively by 11.0% and 8.0%. The application of combined compound fertilizer with composted chicken manure improved soil fertility, and thereby increased rice yield in cold waterlogged paddy fields.