This paper reports the fabrication of gold‐patterned microarray chips for fast and ultrasensitive surface enhanced Raman scattering (SERS) detection of trace samples. By micro‐nano machining based on electron‐beam lithography, magnetron sputtering, and chemical modification, gold‐patterned microarray chips with hydrophilic and hydrophobic periodic structures are fabricated, and a polyethylene glycol (PEG) layer is coated on the surface of the gold well, making the chips long‐term stable. The hydrophilic surface of each gold well is surrounded by a hydrophobic layer, which makes the ultratrace sample amount for SERS measurement only 0.3 μl. In the detection of malachite green (MG), 4‐mercaptopyridine (4‐MPY), rhodamine 6G (R6G), and melamine, great enhanced SERS signals with the detection limit reaching nM level can be achieved due to the enrichment effect of the periodic structures and the hot‐spots generated between the sandwich structure built on the gold wells. Such gold‐patterned microarray chip is promising in fast and ultrasensitive SERS detection of various chemical and biological species with trace amount.