Aims An 8-week trial was performed to evaluate the differences in the intestinal microbiota and immune function of common carp (Cyprinus carpio)-fed different diets. Methods and Results The fish (initial weight 492 center dot 6 +/- 30 g, n = 270) were randomly divided into three groups with three replicates and were fed earthworms (group A), earthworms + duckweed (group M) or duckweed (group P) respectively. The diversity and dominant microbiota of the intestinal bacteria were detected by denaturing gradient gel electrophoresis, and the abundance of dominant bacteria was quantified by qPCR. Additionally, the activities of some nonspecific immune enzymes and antioxidant enzymes were determined. The results showed that higher diversity and abundance of intestinal microbiota were observed in group M and group P (P < 0 center dot 05). Based on the intestinal microbiota, Cetobacterium was only detected in the intestines of common carp in group A, and Bacillus was identified in groups M and P. Additionally, a higher abundance of Bacteroidetes and Firmicutes was also found in the intestine in group P than in group A (P 0 center dot 05). Interestingly, the higher activities of immune enzymes were detected in intestine of common carp in group M, such as acid phosphatase, phosphatase (AKP), lysozyme, total antioxidant capacity, superoxide dismutase, catalase, glutathione peroxidase. In addition, the lower level of metabolites were also detected, such as nitric oxide and malondialdehyde. Conclusions Our results indicate that the intestinal microbiota and intestinal immunity of common carp were affected by diet. Meanwhile, the results show that a mixed diet can promote and improve the immune function of the omnivorous carp intestine, which suggests that paddy fields might be more suitable for the intestinal health and animal welfare of omnivorous fishes because they contain plant and animal diets. Significance and Impact of the Study As an ecological aquaculture strategy, the rice-fish mode has attracted attention among farmers, researchers and even consumers, especially for the cultivation of common carp in paddy fields. In paddy fields, fish can eat plant- and animal-based diets. However, it is not clear whether common carp feeding on a mixed diet in paddy fields have better intestinal health. This experiment is one of only a few studies performed from the perspective of intestinal micro-organisms and immunity to successfully study the effects of different natural diets on adult common carp. This study also provides a theoretical basis for healthy breeding of common carp in paddy fields.