Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum, is a devastating disease and resulted in yields losses and seed quality decreases in Brassica napus worldwide. However, the molecular mechanisms in oilseed rape response to S. sclerotiorum at transcriptional and post-transcriptional levels are still poorly understood. In current study, two RNA libraries, two sRNA libraries and two degradome sequencing libraries for mock-inoculation and 48 h post-inoculation were performed on Illumina platform. We identified 7,065 differentially expressed genes comparing with mock-inoculation after 48 hpi. These genes were associated with protein kinase, signal transduction (CDPKs, G proteins and MAPKs), TFs, hormones, PR proteins, secondary metabolism, transport. In sRNA-Seq analysis, 77 known and 176 novel miRNAs were identified, however only 10 known and 41 novel miRNAs were identified differentially expressed (DE) miRNAs between two samples. Meanwhile, 80 cleavage sites with 64 miRNAs were predicted by degradome sequencing. Furthermore, 70 DEGs and 20 miRNAs were verified by a quantitative real-time PCR (qRT-PCR) approach. Our results will contribute to further understand B. napus-S. sclerotiorum interactions.