Summary: Heterosis is an important biological phenomenon, and hybrid rice is a successful example utilizing heterosis. Currently, good progress has been made in the transcriptomics and epigenetics studies on heterosis; however, the role of small RNA (sRNA) in heterosis of hybrid rice remains poorly described. Here, we performed sRNA profiling of F1 super-hybrid rice LYP9 and its parents, and identified 355 distinct mature microRNAs (miRNAs) and trans-acting small interfering RNAs (ta-siRNAs), 76 of which were differentially expressed sRNAs (DES). Among these, 36 DES were predicted to target 147 transcripts, of which 91 encoded 78 transcription factors. Further analysis showed that the majority of DES expression levels were negatively correlated with their target mRNAs. Gene Ontology (GO) analysis showed that the target genes of DES were enriched in some important biological processes, including the auxin signaling pathway, in which existed a regulatory network mediated by DES and the ir targets. Most of DES and their targets were localized in quantitative trait loci (QTL) related to important rice agronomic traits including growth vigor, grain yield and stress resistance, suggesting that the interaction between sRNAs and their target genes played an important role in the heterotic phenotypic changes. Our findings revealed that sRNAs might play important roles in hybrid vigor of super-hybrid rice by regulating their target genes, especially in controlling the auxin signaling pathway. The above finding provides a novel insight into the molecular mechanism of heterosis. Overall Design: We constructed six sRNA sequencing libraries and six mRNA sequencing libraries of flag leaves and panicles of the super-hybrid rice Liangyou-pei9 (LYP9) combination at the grain-filling stage. The above hybrid rice combination includes F1 hybrid LYP9 and its parental lines including the male-sterile line Peiai64s (PA64s) and the restorer line 93-11.