To understand the water quality of shellfish culture areas in Lianzhou Bay of Guangxi Province and better guide local fishery production, eight water quality factors of the areas were analyzed with SPSS, namely the water temperature, DO, COD, DIP, DIN, oil, Hg and Chl-a, and principle component analysis method was adopted to determine the major influencing factors and comprehensively evaluate the water quality. The results showed that, during the spawn period (May) and high catch period (October), the first four main components, together accounting for 89.9% and 92.9% respectively of the total variance of the two periods, could be extracted to calculate the comprehensive evaluation function score, and the scores of each measuring period from 2013 to 2015 were respectively 0.220, -0.211, 0.759, 1.028, -0.977, and -0.817, with the score levels representing the pollution degree: water quality of both the spawn period and high catch period of 2013 belonged to class III, that of the two periods of 2014 belonged to class IV, and that of 2015 belonged to class I in spawn period and class II in high catch period. It can thus be seen that the water quality of shellfish culture areas was not stable, with relatively large interannual variations, Hg exceeding standard occasionally, and DIP, DIN and Chl-a being the major polluting factors. Therefore, the culture areas should enhance the management over daily operations and industrial outfalls, better control the discharge of sewage and agricultural waste water, as well as scientifically plan the farming scale in order to prevent shellfish farming pollution.