There are differences in the growth of Mytilus edulis Linnaeus farmed with floating raft,around the Gouqi Island waters in the National Marine Special Reserve of Shengsi Ma'an Archipelago. Growth conditions of Mytilus edulis Linnaeus and its relationship with environmental factors are studied using analysis of variance and correlation analysis with the SPSS 16.0 statistical software. Results show that the chlorophyll content, the concentration of particulate organic matter (POM), and the ratio of POM and suspended particulate matter (SPM), have significant effects on the growth of Mytilus edulis Linnaeus. Among them, the third has the biggest significance. Exploring the impact of POM and SPM distribution from the hydrodynamic point of view, the water flow was monitored by Acoustic Doppler Current Profilers (ADCP) and result shows that suspending facilities in the water like floating rafts of Mytilus edulis Linnaeus would have important effects on water exchange of this area. Tidal velocity gradually increases from the surface to the bottom and velocities of flows facing the rising tide and falling tide are greater than that within the culturing zone. Water exchange within the culturing zone would have influence on the distribution of baits like phytoplankton and POM, and consequently, the distribution of baits would affect the growth of Mytilus edulis Linnaeus. The growth rate of Mytilus edulis Linnaeus outside of the culturing zone is obviously higher than that within the zone. Therefore, appropriately planning the culturing blocks in large scale of mussel culturing zone is desirable by leaving some areas blank as passageways along the tidal flow to improve water exchange within the mussel culturing zone, which has great importance.