Three years of field experiment was conducted to study the effects of rice-wheat rotation and maize-wheat rotation on soil desalination, soil organic carbon (SOC) and aggregates of light salinized farmland in the coastal flat of North Jiangsu Province. The results showed that rice-wheat rotation mode was more beneficial for the soil desalinization in 1 m soil depth. Under the treatment of no-fertilizer application and equivalent nitrogen application, SOC in 0–10 cm of rice-wheat rotation mode were increased by about 83% and 75% compared with those of maize-wheat rotation mode, respectively. The macro-aggregates (>2.0 mm) and the mean wheat diameter were both increased with the cultivated years in two rotation systems, especially in rice-wheat rotation land, the macro-aggregates under the treatment of no-fertilizer application and equivalent nitrogen application were about 11% and 26% higher than those of maize-wheat rotation mode, respectively. The study indicated that rice-wheat rotation mode played a more effective role than maize-wheat rotation mode in soil desalinization, SOC accumulation and the improvement of soil instruction in the coastal saline soils.