Soil nitrate nitrogen (NO3 −-N) accumulation is related closely to NO3 − leaching, which is an important issue in groundwater pollution, especially in intensive agricultural areas with saline soils where volumes of water are used in irrigation to avoid salt accumulation in the root zone. However, in the saline environment in Hai River Basin, China, the importance of detailed research into NO3 −-N distribution in the root zone has not been adequately recognized. Considering the impacts of eco-environmental system N and crop production, the present study aimed at contributing to an understanding of the effects of N application rate on soil NO3 −-N distribution, NO3 −-N residue, N loss, and maize (Zea mays L.) yield in this region. The experiment was a completely one-factorial, randomized layout with 4 N application rates. Plant samples and soil samples from 0 to 100 cm depth were collected 8 and 9 times during the growing season, respectively. Soil NO3 −-N concentration was determined using a Flow Solution IV Analyzer. Soil water content was monitored throughout the season via the soil auger method. Samples of irrigation water and rainfall were collected and analyzed for total nitrogen contents. Maize (Zea mays L.) above-ground, dry matter production, grain yield, and harvest index (HI) were measured. And nitrogen content in plant samples was determined by the Kjeldahl method. Under fertilizer treatment, larger quantities of NO3 −-N were present in the upper soil layer (0–40 cm) at 7 days after fertilization (DAF). From 7 to 37 DAF, NO3 −-N decreased, obviously because of the heavy rainfall together with the increase in the capacity of maize to accumulate N in this period, and a significant decrease in NO3 −-N stock was observed. There was a significant positive correlation between the quantity of NO3 −-N stock decrease and the nitrogen fertilizer application rates during this period. And there was more NO3 −-N accumulated in the lower layers under fertilization treatment at 76 DAF. N fertilizer application also had a great effect on maize yield and the highest yield occurred under the treatment of 70 kg N ha−1. This study showed that the N application rate had a significant effect on maize yield, maybe because of the low initial NO3 −-N content. Higher N application rate increased N uptake, but it also increased NO3 −-N residue and N loss, therefore increasing the risk of NO3 −-N leaching. This study showed the present nitrate application rate (140–180 kg N ha−1) during maize cropping season was excessive in the study area. Nitrogen fertilizer application increased NO3 −-N concentration and stock in 0–100cm soil profile and changed NO3 −-N distribution during maize cropping season. And nitrogen fertilizer application promoted movement of NO3 −-N down the soil profile and increased N loss. But effects of nitrogen fertilization application rate on above-ground dry matter production and grain yield were non-linear. A strictly controlled, site-specific, long-term fertilization study will be set up for the determination of biochemical processes of soil NO3 −-N and for the effective N fertilizer management of the saline soil areas.