Sea surface temperature (SST) was estimated by the index of UK37 of organic compounds in the Sanmen bay sediment. It fluctuated between 15.97℃ and 18.00 ℃ with an average of 17.03℃. The estimated SST was 3.52℃ lower than the annual average temperature measured in the same year but was close to the temperature measured in fall. The research indicated that like the climate in the Eastern Pacific Ocean, on a large scale, the climate in the Sanmen bay was similarly affected by the climate events to a different degree according to geographical location and local climate such as monsoon. Like the Eastern Pacific Ocean, in a similar way in chronological basis, the Sanmen bay responded to the climate events but in a weaker scale. By comparison of the community, biomass, inhabit density and biodiversity of macrobenthos during EI Nio (between year 2002 and 2003) and non-EI Nio (between year 2005 and 2006) periods, the research indicated that certain macrobenthos communities in the Sanmen bay responded to EI Nio events by changing those biological features through oceanic circulation. During EI Nio period, warm Taiwan current strongly flowed into the bay. The species of the macrobenthos community during year 2002 and 2003 correlatively reduced with the intrusive current and with the salinity change. Compared to their correspondent in adjacent seas, both the macrobenthos communities and zooplankton in the Sanmen bay responded to El Nio event more significantly. The macrobenthos community species decreased significantly because a warm water invaded into the shallow bay from the floor and thus changed the temperature and salinity in the bay. On the other hand, zooplankton species, biomass and abundance tended to increase in the period of EI Nio since the invaded warm current carried abundant zooplankton.