According to the concept of Microbial Loop, bacteria and virus play important role in organic matter recycling and energy flowing in marine ecosystem, and meanwhile influence many biogeochemical and ecological processes. Marine bacterial and viral ecology has become hotspot in current studies. The South China Sea (SCS) is one of the largest marginal seas in Northwest Pacific, and has already been proved to be oligotrophic. The SCS has attracted great attention due to its economic and strategic importance in recent years. Although the abundance and diversity of bacterioplankton in coastal waters and northern upwelling regions of SCS are well documented, little is known about bacterioplankton and virioplankton distribution in the central and northern area, especially the area near 18°N in SCS, and further investigations should be carried on to study the ecological functions of microbes in this region. In order to study the ecological distribution and function of bacteria and virus in this area, a cruise was conducted during Spring 2014 and water samples were collected from 27 stations. Water column at each station was divided into five layers, which were 5, 25, 75, 150 and 200 m layers respectively. Water samples were collected by Niskin bottles, fixed with glutaraldehyde and stored at liquid nitrogen immediately. Bacterioplankton and virioplankton abundances at different water layers and stations were measured by flow cytometry method. Horizontal and vertical distribution and its correlation with environmental variables, such as temperature, depth, salinity, dissolved oxygen, chlorophyll a and inorganic nutrients were also analyzed. The results showed that the bacterioplankton and virioplankton abundances in the upper 200 m of the water column were 1.28×10⁴-9.96×10⁵ cells/mL and 4.69×10⁵-5.39×10⁷ cells/mL, respectively. Their abundances were similar to the results in other oligotrophic oceans and lower than that of the coastal areas. With the increase in water depth, the abundances of both bacterioplankton and virioplankton decreased gradually in the vertical direction and in correlation with the euphotic layer, but no significant distribution pattern was detected in the horizontal direction. The variation in bacterioplankton and virioplankton abundance was significantly correlated with water temperature, pH, and dissolved oxygen, but negatively correlated with water depth, salinity, active phosphorus, silicate, nitrate, and total nitrogen (P<0.01). We conclude that bacterioplankton and virioplankton abundances were regulated by multiple environmental factors. Virus-to-bacteria ratio (VBR) reflects the relationship between bacteria and virus. The average VBR in this region was 32.23. The maximum value was 264.63 and it was observed at the 75 m layer of S7 station. The minimum value was 4.80 and it was detected at the 25 m layer of S11 station. A VBR value lower than 100 was detected in 95.6% of the stations. No significant correlation was found between VBR and environmental variables (P>0.05), however, a significant negative correlation was observed between bacterioplankton and VBR (P<0.01). A strong correlation between bacterioplankton and virioplankton was detected (P<0.01), indicating that bacterioplankton is probably the main host of virioplankton, and the virioplankton probably mainly existed in the form of bacteriophage. Relationships between organic carbon and bacterioplankton need to be further studied in order to illuminate growth and decline mechanism of microbes in SCS.