Hypoxia (DO<2mg/L or <30%) often caused acute mass fish mortality within 12 days in cage culture area of Laoyehai Lagoon (Hainan, South China Sea) during spring drought. To understand the causes of hypoxia, we conducted 7 cruises in biogeochemistry in the area during 20082011. The 2009 cruise was conducted in spring monsoon transition period during which wind speed was high and rainfall ample, bottom hypoxia was rare; correspondingly, water column was unstable in vertical direction in the whole lagoon, phytoplankton community was dominated by pico-phytoplankton (<2mum) and nano-phytoplankton (210mum) species. The 2010 cruise was in spring monsoon transition period featuring breeze and drought, and bottom hypoxia was common from the deep hole (depth of about 6m) in the inner bay to the cage culture area in the outer bay; correspondingly, water column structure of the deep hole was strongly stratified, phytoplankton community was dominated by diatom Cerataulina pelagica, and virus abundance reached the highest value of all 7 cruises. The cruises conducted in 2008, 2009 and 2011 met southwest monsoon periods during which weather was hot with breeze and ample rainfall; bottom hypoxia was in small scale, and the hypoxic water mass was limited to the deep hole; correspondingly, water column structure of the deep hole was highly stratified, phytoplankton community was dominated by pico-phytoplankton (<2mum) and nano-phytoplankton (210mum) species. These results show that hypoxia phenomena in Laoyehai Lagoon responded clearly to the rhythmic climate change of the South China Sea Monsoon, and to the coupling between the stratification and diatom bloom in water column of the deep hole, which was caused by spring drought and resulted in massive hypoxia spread from the deep hole in the inner bay to the cage culture area of the outer bay.