Early development is a key process of fish regulated through dynamic and complex mechanisms that involve various gene functions. MicroRNAs (miRNAs) play a major role in the post-transcriptional regulation of target genes. Bighead carp (Hypophthalmichthys nobilis) is a native and important aquaculture species in China, whereas the genetic regulation basis related to the early development is not available. Here, we propose the first developmental regulation profiles by miRNA-sequencing, to study their dynamic regulation during early development in bighead carp.