In this work, we demonstrate a novel rotary microsystem for simple, rapid and automatic influenza viral RNA purification. The microdevice consists of a silica sol–gel matrix for RNA capture, and three reservoirs for a RNA sample (R_S), a washing solution (R_W) and an elution buffer (R_E) that were connected with different dimensional microfluidic channels (120 μm for R_S, 40 μm for R_W, and 20 μm for R_E). The hydrophobic property of PDMS and the narrow microchannel served as a passive capillary microvalve, and the loading of the solutions were controlled by centrifugal force. 5 μL of a lysate sample of influenza A H1N1 virus, a washing solution and an elution buffer were injected in each designated reservoir, and the virus sample, the washing solution, and the elution buffer were sequentially loaded into the sol–gel chamber at 1600, 2000, and 2500 RPM, enabling the viral RNA to be captured in the sol–gel solid phase, purified, and eluted in 5 min. The RNA capture yield was measured as 80%, and the H1 and M gene were successfully amplified from the recovered purified H1N1 viral RNA by reverse-transcriptase PCR. Such a novel rotary sample preparation system eliminates any complicated hardware and human intervention, and performs the RNA extraction with high speed and high fidelity.