The invention provides a flexible SOI device structure and a preparation method thereof; the flexible SOI device structure sequentially comprises a flexible substrate, a first back gate region, a second back gate region and an inter-back-gate isolation part, an insulating buried layer, a first active region, a second active region and a device isolation part, an interlayer dielectric layer and a contact hole from the bottom up, wherein the first back gate region, the second back gate region and the inter-back-gate isolation part are located above the insulating buried layer; each of the firstactive region and the second active region comprises a gate region, a body region located below the gate region, and a source and a drain which are located at the two transverse ends of the body region respectively; the interlayer dielectric layer is located at the highest position; the contact hole runs through the interlayer dielectric layer, the device isolation part and the insulating buried layer in sequence; and the contact hole is filled with a conductive material to form a contact part, and the first back gate region and the second back gate region are applied with a bias voltage by the contact part, wherein the first back gate region and the second back gate region are electrically isolated from each other by the inter-back-gate isolation part. According to the structure, the inter-back-gate isolation part is added to realize independent modulation of the back gate device; and meanwhile, the flexible preparation of the flexible SOI device structure is realized.