The wetland of the Yellow River estuary is a typical new coastal wetland in northern China. It is essential to study the carbon pool and its variations for evaluating the carbon cycle process. The study results regarding the temporal-spatial distribution and influential factors of soil organic carbon in four typical wetlands belonging to the Yellow River estuary showed that there was no significant difference in the contents of the surface soil TOC to the same season among the four types of wetlands. For each type of wetlands, the TOC content in surface soils was significantly higher in October than that in both May and August. On the whole, the obvious differences in DOC contents in surface soils were not observed in the different wetland types and seasons. The peak of TOC appeared at 0–10 cm in the soil profiles. The contents of TOC and DOC were significantly higher in salsa than those in reed, suggesting that the rhizosphere effect of organic carbon in salsa was more obvious than that in reed. The results of the principal component analysis showed that the nitrogen content, salinity, bulk density, and water content were dominant influential factors for organic carbon accumulation and seasonal variation.