The invention discloses an aspiration system for thrombus in a blood vessel. The aspiration system comprises an aspiration conduit capable of being implanted into a human body via percutaneous, and a driving module. The aspiration conduit comprises a blood entrance port, a blood flow channel and a blood outlet; a filter net is disposed in the blood flow channel of the aspiration conduit; an impeller is arranged between the filter net and the blood outlet or on the blood outlet; and the impeller is connected with the driving module. Blood flow interdiction is unnecessary for the aspiration system for the thrombus in the blood vessel; with a negative pressure aspiration way, the thrombus can be safely taken out and thrombus crack and falling-off can be prevented; compared with an aspiration conduit technology in the prior art, patient blood flows back to a blood circulation via the filter net, so blood loss can be avoided by the use of the aspiration conduit; and thrombus can be pulled out when the conduit is removed.