In this study, the δ13CPOM and δ15NPOM values in the southern SOJ were investigated and reported for the first time. Our observations were mostly conducted in the summer, therefore our identified characteristics of δ13CPOM and δ15NPOM mainly reflected the characteristics of the summer of SOJ, while seasonality, except autumn, was covered by the monitoring line. There were significant seasonal variations in δ13CPOM and δ15NPOM in the surface mixed layer, but not below the mixed layer (at 30 m depth). Environmental variables and primary production processes adequately explained the observed δ13CPOM value. δ13CPOM could be estimated using our GLM and routine hydrographic observations. However, environmental variables did not adequately explain the variation in δ15NPOM. In particular, the relationship between nitrate concentration was not found. The SJO contains different nitrogenous sources, such as atmospheric depositions and riverine inputs, and δ15NPOM indicates that these sources are mixed and support primary production. The simulation supported that multiple nitrate sources contributed to the ambiguous relationship between δ15NPOM and nitrate concentration. The main nitrogen source in the SOJ was not detected in our study, but the new production was dependent on the nitrate supplied from these sources. Anthropogenic nitrogen inputs were increased in the SOJ (Duan et al., 2007; Kitayama et al., 2012), and hence, the new production in the SOJ is expected to increase. As a result, we must evaluate the impact of “increased” new production on the biogeochemical cycles and ecosystems in the SOJ.