Effects of immobilized microorganisms on regulation of water quality and bioremediation of polluted sediment in Litopenaeus vannamei aquaculture ponds were studied by measuring algae community structure, various water quality parameters, total organic carbon(TOC) of sediment and heterotrophic bacteria. Immobilized microorganisms included microorganisms immobilized by zeolite(ZE-M) and biological active carbon(BE-M). The results showed that the algae were more diverse, with similar proportions of cryptophyta, bluegreen and green algae in the ponds with immobilized microorganisms, while bluegreen algae dominated in the control ponds. Concentration of ammonia nitrogen and COD increased linearly with culture time in the control ponds, but increased more slowly in the treatment ponds, which was probably due to the application of immobilized microorganisms of ZE-M and BE-M. Other indices of water quality did not show significant difference between treatment and control ponds. Effects of immobilized microorganisms on TOC content in the sediment and amount of heterotrophic bacteria were significant(P<0.05). TOC content in the sediment in both treatment and control ponds increased with culture time, but TOC content in the control ponds increased more rapidly. At the beginning of the experiment, the amount of heterotrophic bacteria was 3.367×10⁵-8.60×10⁵ CFU/g, and increased to 85×10⁵-393.7×10⁵ CFU/g by the end of the experiment. The amount of heterotrophic bacteria between treatment ponds and control ponds was significantly different(P<0.05) with the lowest amount in the ZE-M group(21.59% of the amount in the control ponds). Our study showed that immobilized microorganisms could significantly improve water quality, increase algae biodiversity and bioremediate polluted sediment in Litopenaeus vannamei aquaculture ponds.