The invention discloses an ultra-sensitive homogeneous electrochemical aptamer sensor used for thrombin detection and based on a graphene signal amplification effect, which is embodied in that a nanometer hydroxyapatite (HAP) modified with an aptamer 2 as a signal probe and magnetic microspheres modified with an aptamer 1 can form the ultra-sensitive homogeneous electrochemical aptamer sensor in the presence of target object thrombin. Graphene oxide generates reduced graphene oxide on the surface of a glassy carbon electrode by means of electrodeposition, and graphene plays a role of signal amplification. The HAP in a sandwich structure with the target object thrombin and sodium molybdate solution form a phosphomolybdate precipitate with redox electrical activity on the graphene surface. Detection and characterization are performed by electrochemical methods. Results show that in a homogeneous solution, a sensitive effect on the detection of the thrombin is achieved. In the optimal detection environment, the response to the thrombin presents a linear range, ranging from 1 nM to 1 fM, with a detection limit of 1.3 aM.