A 3-year pot trial was conducted to demonstrate the relationship between rice grain yield and biochar-amended soil properties together with carbon storage in the Yangtze River estuary, China. Straw biochar was incorporated once into soil in pots at five different rates: 0%, 5%, 10%, 15%, and 20% (dry biochar weight/wet soil weight). Compared to yields from the control treatment with no biochar, rice grain yield was improved by 29.1-34.2% in the treatments with 10-15% biochar in the first year following biochar application. In the second year following biochar application, the rice yield was increased by 51.8-96.0% in the treatments with 15-20% biochar. However, compared to the control treatment, hardly any yield increase occurred in any of the biochar treatments in the third year following biochar application. Higher amounts of added biochar increased the soil organic carbon (SOC) and total nitrogen (TN). SOC contents were invariable and increased nearly 60-250% annually in the biochar treatments compared with the control. Biochar increased soil TN 22.9-75.3%, 24.0-60.9% and 13.8-51.2%, respectively, in each of three consecutive years. Biochar increased the mean concentrations of EC, RAP, RAK and DOC by 8.8-44.8%, 10.0-61.1%, 65.6-310.1% and 9.1-20.0%, respectively, during the three rice-growing seasons. The addition of 10-15% straw biochar to soil and regular annual biochar supplements for agronomic purposes is a potentially sustainable management technology to enhance coastal mudflat soil properties and improve rice yields therefrom.