The seasonal variations in shelf circulation and their implications for the distribution of light fishing vessels positions (VBD) that capture small pelagic fishes in the southern South China Sea (SSCS) are investigated by using multi-datasets between 2008–2014. It is found that the SSCS shelf circulation is indicated by the strong seasonal reversal western boundary current (WBC) and prominent cyclonic circulation (eddy). The southeastward WBC brings homogeneous salty, colder, and high primary production of nanophytoplankton (PPN) water during winter-time from the northern and the cyclonic eddy region into the southern SSCS. In contrast, less salty, warmer, and less PPN are advected northwestward from Karimata into the northern region. These factors significantly influence the distribution of VBD and in turn the production of captured small pelagic fishes (CPUE), revealing two maxima (peaks) of both VBD and CPUE during the monsoon breaks (MB) with a time-lag of 2–3 month from the monsoon peaks. Relationship between oceanographic parameters and CPUE is examined statistically revealing that ocean current and PPN are significantly affect the CPUE. A relatively high PPN and strong current during the peaks of monsoon are correlated with lower CPUE. In contrast, during the MBs period CPUE maxima are associated with a relatively weak ocean current and consumed PPN that favor the abundance of small pelagic fishes.