Powdery mildew, known as one of the most devastating diseases in cereal crops, causes serious losses in grain yield and quality. In order to clarify the pathogenic molecular mechanism of qingke barley to powdery mildew, In the present study, the DEGs expression patterns of Tibetan barley (also called qingke) cultivars G7 (showed complete penetration resistance to powdery mildew) and Z13 (showed complete penetration sensitivity to powdery mildew) were compared after inoculation with Blumeria graminis f. sp. Hordei (Bgh). The genes coding for calcium-dependent protein kinase, glutathione S-transferase, plasminogen activator inhibitor 1, serine-type endopeptidase, and MADS-box transcription factor were expressed at higher levels in the G7, indicating their possible roles in the resistance to Bgh. The highly expressed genes in G7 take a part in the biological processes including ion channels, calcium-dependent protein kinase, and plant hormone pathway. Sixteen lncRNAs and their 21 candidate target genes were identified to exhibit coordinated expression patterns, which were enriched in plant hormone signal transduction and ion binding processes. This study casts an insight into the molecular mechanisms to control powdery mildew in barley and relative species.