The distribution of nektons in aquaculture areas is the result of the interaction among nektons, environmental loads and hydrological conditions of culture areas. Thus, it is speculated that the corresponding relationship between the distribution of nektons and aquaculture types is diverse and uncertain. To verify this inference, trap nets were used to collect nektons in the aquaculture areas with different types and their adjacent waters in Sansha Bay, Fujian Province. The results showed that the composition of nektons characterized by species number, Chao 1 index, Shannon-Wiener diversity index, Margalef richness index, Pielou evenness index, key species and dominant species did not exhibit specificity to the types of culture areas; the similarity of the communities of nektons in the aquaculture areas with different types characterized by the key species and dominant species was relatively small, but the community similarity based on all the species of nektons was≥0.84; there was no correlation between the composition of nektons and the types of aquaculture area, and the biological community of nektons did not change with aquaculture area. Thus, it is not reasonable to evaluate the biological effects of cage culture by using the commonly used spatial comparison method, and it is suggested to adopt the adaptive management to manage cage culture.