Through correlation of nannofossils from one well in the northern continental shelf of the South China Sea and DSDP site 296, and by comparison of this study with Lohmann and Carlson (1981) and Ellis (1973) on Tertiary nannofossils distribution of the Pacific region, the author has discovered that the nannofossils in the Tertiary marine sequence in the shelf region of the marginal sea differ from those in the open ocean, mainly in the lower abundance and diversity, higher amounts of small-sized nannofossil, higher content of Sphenolithus and Helicosphaera, and lower content of Discoaster. The causes of these differences are also discussed.