We have set up a novel quasi-3D structure, periodic arrays of two-layer coupled quadrate-holes and squares. SERS measurements show that for 514 nm excitation the average enhancement factor of periodic arrays of the coupled structure over the normal Ag film can reach 4 x 10(2), much higher than the known experimental result for periodic arrays of nanoholes. The simulation shows that the SERS enhancement caused by the coupled two-layer structure is about 2.4 orders of magnitude higher than that of a simple one-layer structure, which verifies the advantages of the structure with two-layer coupled pairs of quadrate-holes and squares over the structure with one-layer nanoholes for SERS measurement.