The effects of fermentation bed paddings partially replacing chemical fertilizer on crop aboveground biomass, N efficiency, soil fertility and heavy metals contents on Italian ryegrass–rice rotation were studied to explore the suitable replacement ratio of organic fertilizer and chemical fertilizer under rice-ryegrass rotation, and to construct the safe application technology of organic fertilizer, which can provide technical support for high-yield and high-efficiency crop production under grain-grass rotation system in southern agricultural areas. Under the condition of equal nitrogen application, a field experiment was carried out in two years, in which 6 fertilization treatments were setup: CK, no fertilizer treatment; inorganic fertilizer treatment (T1), fermentation bed paddings replacing 25%, 50%, 75% chemical N (T2, T3, T4), and fermentation bed paddings (T5). The effects of different treatments on the aboveground biomass, nitrogen use efficiency, soil physiochemical properties and heavy metal contents were determined. The results showed that compared with CK, all fertilization treatments improved rice grain yield and straw yield, Italian ryegrass yield and annual aboveground yield. In the treatments with different proportions of organic fertilizer, with the increase of proportion of organic nitrogen substitution, crop yield showed a decreasing trend. The experimental data for two consecutive years showed that compared with T1, T2 increased the annual aboveground yield of by 5.88% and 6.40%, but there was no significant difference between T3 and T1, and significantly decreased in the T4 and T5 treatments. [The total annual crop yield of Italian ryegrass–rice rotation showed an increasing trend with the increase of the application ratio of fermentation bed paddings] the annual shoot yield of T4 and T5 increased by 11.49% and 20.34% respectively in the second year compared with the first year. Nitrogen uptake and use efficiency of rice and ryegrass were significantly increased by applying appropriate proportion of organic fertilizer. Nitrogen uptake of rice grain and straw as well as ryegrass were the highest in T2, while there was no significant difference between T3 and T1, but T4 and T5 significantly decreased. Compared with T1, T2 increased the aboveground nitrogen uptake by 9.387% and 7.59%, and increased nitrogen use efficiency by 14.66% and 10.14%, increased partial productivity by 7.58% and 5.94% in the first and second year respectively. Soil pH and the contents of organic matter, available potassium and phosphorus increased with the increase of the proportion of organic fertilizer, while the content of available nitrogen increased first and then decreased. According to the two-year average value, compared with T1, T3, T4 and T5 increased the SOM contents by 33.98%, 46.23% and 47.09%, and increased available phosphorus contents by 49.11%, 67.15% and 73.87%, and increased available K contents by 23.36%, 36.77% and 55.24% respectively. The application of organic fertilizer resulted in the enrichment of Cu and Zn in soil, but had no significant effect on Cd content in soil. The contents of Cu, Zn and Cd in the same fertilization treatment were lower in the first crop year than in the second crop year, but the contents were all within the soil pollution risk control standard (GB15618—2018). In conclusion, 25%-50% of the fermentation bed paddings and inorganic fertilizers applied is suitable for Italian ryegrass–rice rotation in the Yangtze River.