The invention discloses a chondroitin sulfate separating device with a filter structure. The chondroitin sulfate separating device comprises a liquid supply pipeline and resin columns, wherein one end of the liquid supply pipeline allows bone soup with the temperature higher than normal temperature to enter the liquid supply pipeline, the middle section of the liquid supply pipeline is bent to form a filter pipe section, the filter pipe section is formed by a plurality of U-shaped sections which are sequentially connected, two close upper ends of the two adjacent U-shaped sections are connected, a filter disc structure is arranged on the inner wall of the lower bent part of each U-shaped section, and the filter disc structure at least partially block the U-shaped section; each filter disc structure is provided with a fleece layer on one side facing the flowing direction of the bone soup, the fleece layer is formed by fibers produced by plastics, one end of each fiber is connected to the filter disc structure, and the other end of the fiber extends outwardly; each resin column is provided with a liquid inlet in the top and a liquid outlet in the bottom, and the other end of the liquid supply pipeline is communicated to the liquid inlets of the resin column. The chondroitin sulfate separating device has the advantages that separating efficiency is increased, and the structure of the device is simplified.