In order to characterize the bacterial community structure and diversity in rearing water of healthy Litopenaeus vannamei larvae during hatchery period, the genomic DNA of aquatic microbiota from larval stages of nauplius 5 (N5), zoea 2 (Z2), mysis 1 (M1) and postlarvae 1 (P1) was amplified with 16S rDNA V4 primers and sequenced by a high-throughput Illumina MiSeq platform. The results showed that the bacterial Shannon diversity index increased at P1 stage after declining gradually from stages N5 to M1, the Pielou evenness index at N5 stage was a little higher than those of the following three stages, which were approximated closely. During the entire larviculture period, the phylum Proteobacteria was overwhelmingly dominated in rearing water with high abundance up to 50.0%-88.0%, especially, the family Rhodobacteraceae of which had high abundances of 24.2%, 61.6%, 43.3%, and 51.8% at stages N5, Z2, M1, and P1, respectively. Bacteroidetes thrived in various stages with abundance higher than 9.7%, and the family Saprospiraceae of this phylum existed significantly (5.3%-16.9%) in the latter three phases. Actinobacteria presented also dominantly in rearing water except for the N5 stage, and the family Microbacteriaceae with abundances of 5.6%, 37.6% and 10.8% for Z2, M1, and P1 stages, respectively. The phylum Verrucomicrobia dominated only at P1 stage (5.3%). In the larviculture water, the core microbiota at genus level consisted of Loktanella, Marivita, Donghicola, Sulfitobacter, and two unclassified candidates. Thus the microbiota in larval rearing water harbored a high diversity and presented dynamic succession, which differed obviously between N5 stage and the latter three stages. Overall, the main environmental factors in larviculture water varied slightly and exhibited no significant effect on abundance of dominant OTUs (operational taxonomic units). In conclusion, the bacterial community in rearing water of healthy L. vannamei larvae shifts in composition and abundance with larval development and diet feeding. And the core microbiota with potential functions play an important role in maintaining homeostasis in the larviculture system, which could serve as candidates for autochthonous probiotics, as well as healthy indicator for shrimp larviculture.