[Background] Systematically understanding the distribution of saline soil nutrients and salts on both sides of the mouth of Huai River is important in establishing strategies for soil salinity management. [Methods] In this paper, the spatial distribution characteristics of soil nutrient indexes, i. e. , soil organic matter (SOC), available nitrogen (AN) and available phosphorus (AP), and salinity mass fraction for various depth layers (0 -10 cm, 10 -20 cm, 20 -50 cm, 50 -100 cm, 100 -150 cm, 150 -200 cm, 200 -250 cm, 50 -300 cm and 300 -350 cm) at the estuary of Huai River were analyzed by the application of Outdoor survey and sampling as well as indoor analysis, including cluster analysis and correlation analysis. [Results] 1) The research area was generally lacking in SOC and AN, the amounts of SOC and AN presented a slow increasing trend with the increasing distance from the estuary, while the amount of AP was appropriate in general. Soil nutrients showed an obvious surface aggregation phenomenon, compared with the floodplain, the variation depths of SOC and AN in the soil on the dike outer were low, while the difference of AP was not obvious. 2) The amounts of salinity in the research area presented a slow increasing trend with the increasing distance from the estuary. The critical desalinization positions of the north floodplain, south floodplain, north dike outer and south dike outer were respectively located at 3200 m, 2800 m, 3400 m and 600 m from the estuary. The salinity profile types were obviously classified into the types of surface accumulative, bottom accumulative and balanced,the distributions were concentrated and respectively located in the severe salinization zone, moderatesalinization zone, mild salinization zone and desalinization zone. 3) SOC and AN presented highly significant positive correlation, and the two had significant negative correlation with the soil salinity, while AP was not significantly correlated with the other three indexes. [Conclusions] The research results can serve as a theoretical and practical reference to the partition, amelioration, management and rational utilization of saline soils in the estuary of Huaihe River.