From April to November, 2014, an in situ nitrogen (N) loading experiment (N0, no N loading treatment; N1, low N loading treatment; N2, moderate N loading treatment; and N3, high N loading treatment) was conducted in a Suaeda salsa community in high marshes in the northern Yellow River estuary. Different N-substrate seeds were sampled in the corresponding N treatment plots (S0, S1, S2, and S3). The objective of this study was to explore the responses of germination and seedling growth of different N-substrate seeds of S. salsa to salinity stress and nitrogen loading. Results showed that the N content in seeds sampled from different N loading plots were in the order of S2 > S0 > S1 > S3 and compared to other N loading treatments, the N2 treatment was more favorable for N accumulation in seeds. The interaction of salinity stress and N concentrations showed substantial effects on germination rate of the four N-substrate seeds, following the sequence of S2 > S1 > S0 > S3 (P > 0.05). Under different salinity stresses, the germination rate and seedling growth of S2 were the best. With increasing salinity, the germination rate and seedling growth of the four N-substrate seeds were generally inhibited, but at lower salinity, conditions were favorable for seedling elongation and the inhibitory effect could be alleviated by high N loading. The combined effect of salinity stress, N concentration, and seed types had significant impacts on germination rate, seedling length, and fresh and dry weight. Except for seedling length, the interaction of the three factors demonstrated no significant influences on the above ecological traits. This study found that the N loading treatments not only altered the nitrogen content of S. salsa seeds in the primary environment, but also resulted in N-substrate seeds that presented different adaptation strategies to nitrogen loading and salinity stress. Compared to other N-substrate seeds, S2 showed great advantages in germination rate and seedling growth. In the future, nutrient loading will be increasingly utilized in the newly created marshes of the Yellow River estuary. It was concluded that, as the nutrient reached the N2 level, germination and seedling growth of S. salsa would be greatly promoted. If nutrients reached higher levels, germination and seedling growth would, to some extent, be inhibited.