The profound interplay between intestinal microbiota and animal biology has received ample scientific attention. Yet the alternations of microbiota populating the fish intestine with respect to starvation remain incompletely understood. The present study used 16S rRNA sequencing to investigate changes of intestinal microbiota in grass carp (Ctenopharyngodon idellus) during starvation. The microbial community structure of starved fish differed from that of the fed fish (day 0 of the experiment) (F = 25.8, PERMANOVA P = 0.0001). Compared with the fed fish, starved fish had a higher abundance of Vibrio and a lower abundance of Bacteroides, Fusobacterium, Coprococcus and Citrobacter genera. Predicted functions indicated that microbiota changed the specific metabolic pathways and functions to adapt to the food deprivation. The expression of TLR3, TLR5b, TLR7, IL-1 beta, and TNF alpha genes was generally up-regulated, MyD88 slightly down-regulated, and IL-8 almost unchanged in response to starvation. Statistical analyses indicated that the expression of three genes associated with inflammatory responses, namely TLR5b and IL-1 beta (both separately and combined), as well as TNFa, was significantly positively correlated with the composition of microbial communities populating the grass carp intestine during starvation. This suggests that changes in microbial composition might stimulate inflammatory responses. Taken together, starvation alters the structure and function of microbial communities and also influences the intestinal immune system and stimulates inflammatory responses of grass carp.