Both primary production (PP) and bacterial production (BP) are key basic biological productions in marine ecosystems. In this study, the basic biological productions in different zones in the northern South China Sea were investigated in summer in 2008, in order to evaluate the spatial distribution characteristics of the basic biological productions, their influencing factors and their contributions to the carbon flux in the ecosystems of the South China Sea. The investigation covered the estuarine and Yuedong coastal area, the adjacent area of Taiwan Strait and Luzon Strait, the southeast waters of Hainan Island, and the open waters in the northern South China Sea. The results showed that the surface PP (C) and the integrated PP in the euphotic zone (IPP) (C) were (0.83±1.15) mg?m-3?h-1 and (225.39±136.64) mg?m-2?d-1 respectively; the average surface bacterial production (C) and the integrated bacterial production (IBP) (C) in the euphotic zone were (0.14±0.19) mg?m-3?h-1 and (128.14±74.86) mg?m-2?d-1 respectively. The basic biological production generally declined from the nearshore waters to the deep sea. Besides the general distribution of high production in coastal and estuarine waters, high PP area could also be found near the Xisha Islands. The high PP value usually appeared in the deep water other than in the surface layer with two vertical peaks in the euphotic zone, one at the depth of 0-20 m and another at the depth of 50-75 m in most stations in the open water of the northern South China Sea. According to the vertical distribution of BP, maximum BP values appeared mostly near bottom layers of the euphotic zone (50-75 m). The correspondence analysis between BP and environmental parameters indicated that temperature and nutrients are not key controlling factors of BP in the northern South China Sea; BP was significantly correlated with phytoplankton biomass and PP. The IBP: IPP ratio averaged 67.55 37.13% and had a significant negative correlation with PP, which indicated that in the northern South China Sea, phytoplankton photosynthesis could afford enough carbon resource to the ecosystem in the high PP area in the euphotic zone, while in the area with low PP, the bacterial production process appeared to be more active. Microphytoplankton and nanophytoplakton was often the primary contributor to PP in the coastal area accompanying with the distribution of low BP∶PP and IBP∶IPP, which indicated that the classic food chain was the main approach for the basic carbon flux in the coastal waters of the northern South China Sea. However, in the oligotrophic open waters that cover most area of the northern South China Sea, IBP: IPP was evidently higher than that in the nearshore waters; the area with extreme high IBP: IPP ratio (>100%) was found in part of the deep sea area. Meanwhile, picophytoplakton was the dominant primary producer in the oligotrophic waters in the South China Sea, which suggested that heterotrophic bacteria and picophytoplakton play important roles in the ecosystem carbon cycle transporting carbon flux via the microbial loop to higher nutrition levels in the oligotrophic waters of the South China Sea.