The "in-out" stepwise regression method is adopted to analyze the significance of environmental factors having influence on phosphorus nutrient variation and their influencing weights in the East China Sea. The results showed that the relative importance of environment factors influencing phosphorus nutrient variation in the East China Sea is as follows: silicate > nitrate > temperature > dissolved oxygen > nitrite > pH > salinity > basicity > ammonia salt, with the relative influencing weights being 18.01%, 17.84%, 15.17%, 10.98, 8.43%, 7.9%, 7.63%, 7.53% and 6.52 % respectively. That the influence of silicate on phosphorus nutrient variation is relatively great explained the structural changes of phosphorus nutrient and silicate played a vital role in the evolution of phytoplankton community. It also agreed with the fact that the red tide causative species have been evolving from medium-type (mainly diatom) to mini-type (mainly inoflagellate). Some environment factors such as silicate will, therefore, be taken into account to build the dynamics model of phosphorus nutrient and marine ecological model in the future.