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Coastal lands are often affected by salinization, which leads to a deterioration of soil structure and a decrease in land productivity. As a widely used soil amendment, biochar has been proven to improve poor soil properties and promote crop growth and N adsorption and utilization. However, the effects of biochar on soil fertility, N use efficiency (NUE) and balance in coastal salt-affected soil have rarely been reported. Therefore, we conducted a field micro-plot experiment to study the improvement effects of different biochar rates (0, 13.5, 20.25 and 27 t/ha, corresponding to CK, B1, B2 and B3 treatments, respectively) on coastal salt-affected soil. The results showed that biochar application increased soil water content (SWC) in seasons with abundant rainfall but decreased SWC in seasons with strong evaporation, and the increase or decrease in SWC was greater with the increase in biochar rates. Biochar application increased soil salinity and decreased soil pH, although high rates of biochar increased soil salinity to a lesser extent, while low rates of biochar decreased soil pH most. Biochar application was able to reduce soil bulk density, while B1and B2 treatments decreased it to a higher degree. Moreover, biochar application increased soil macro-aggregates (>0.25 mm) and organic matter, while B2 and B3 treatments increased it to a higher degree. Biochar application improved soil fertility to an extent that crop grain increased yield by 2.84~19.88% in barley season and 12.27~16.74% in maize season. Meanwhile, biochar application also increased NUE because it promoted the increase of yield. In particular, the calculation of N balance between soil and plant systems suggested that biochar application could reduce the apparent N loss during crop planting, and B1 treatment was better at reducing apparent N loss. Overall, our study indicates that biochar application has great potential to improve poor physicochemical properties and N nutrient utilization in coastal salt-affected soil. More importantly, we suggest that biochar application rates should be controlled in coastal salt-affected soil.