An attempt was made in the present paper to develop a nanoporous gold (NPG)-based electrochemical aptasensor for thrombin detection. The substrate electrode NPG was in situ fabricated by a facile one-step square wave potential pulse (SWPP) treatment. The treatment involved repeated gold oxidation-reduction and intensive H(2) bubbles evolution. After 100min treatment, the active surface area of Au increased greatly (34 times). The electrochemical aptasensor was fabricated using a layer-by-layer assembling strategy. A "sandwich" structure was formed via thrombin connecting the aptamer-modified NPG and the aptamer-modified Au nanoparticles (AuNPs). The AuNPs was modified with two kinds of single strand DNA (ssDNA). One was aptamer of thrombin, but the other was not, reducing the cross-reaction between thrombin and its aptamer on the same AuNP. The electrochemical signal produced by the Ru(NH(3))(6) bound to ssDNA via electrostatic interaction was measured by chronocoulometry. Due to the amplification effects of both NPG and AuNPs, this novel NPG-based aptasensor could detect thrombin quantitatively in the range of 0.01-22nM with a detection limit as low as 30fM. The present aptasensor also exhibited excellent selectivity, stability and reusability.