In this paper, salt-tolerant wheat and rice were used as materials to study their growths and yields under nutrient-balanced fertilization systems in seashore saline-alkali farmland in the reclamation area in Zhong Road Port of Dafeng County, Yancheng City, Jiangsu Province. The designed treatments included no fertilization (CK), conventional fertilization (TF), medium element fertilizer + conventional fertilization (TS), chelated trace element fertilizer + conventional fertilizer (TM) and medium element fertilizer + chelated trace element fertilizer + conventional fertilization (TSM). The results showed that in wheat season, TSM significantly increased soil alkaline nitrogen and available potassium contents by 23.22% and 7.10% respectively compared with TF. In rice season, TSM also significantly increased soil available phosphorus and potassium by 19.78% and 7.44% respectively compared with TF. TSM significantly reduced soil salinity from 3.09 g/kg to 1.88 g/kg in rice-wheat rotation system. In wheat season, TSM significantly increased soil S and Fe contents by 196.3% and 13.75% respectively compared with TF. In rice season, TSM significantly increased soil Si, Ca, Fe, and Mn contents by 27.42%, 11.60%, 12.05% and 16.20% respectively compared with TF. Compared with TF, TSM significantly increased wheat and rice biomass by 19.47% and 20.12% respectively, and also significantly increased nutrient contents in different organs. Fertilization increased the accumulation of nutrients in different organs of rice and wheat and promoted crop yields, TSM significantly increased wheat and rice biomass by 14.37% and 46.46% respectively compared with CK. Wheat yield was increased by 7.55% whereas rice yield changed insignificantly compared with TF. In summary, balanced fertilization effectively improved nutrient storage capacity and nutrient utilization efficiency, therefore promoted the growth and yield of rice and wheat. Thus, adding medium and trace elements in conventional fertilizers is the optimal balanced fertilization model for seashore saline-alkali farmland.