The development of a thin film with well-defined metallic micro/nanostructures, diverse surface functionalities, and superior electronic/optical properties has been a great challenge to researchers seeking an efficient method for the detection of various analytes in chemical and biological sensing applications. Herein, we report a facile and effective approach to the fabrication of an ordered gold island pattern on a glass substrate with contrasted chemical functionalities, which can provide spatially separated sensing zones for multi-detection. In the proposed method, the combination between the micro/nano-imprint lithography and sequential self-assembly approaches exhibited synergistic effects that allowed well-defined structuring and easy surface functionalization in separated sensing zones. Via imprint lithography, the uniform gold islands/glass structure was successfully fabricated from a readily available gold-coated glass film. In addition, a sequential self-assembling strategy and specific chemical-substrate interactions, such as thiol-gold and silane-glass, enabled the surfaces of gold islands and exposed portions of the glass substrate with contrasting chemical functionalities-SH-functionalized gold islands and NH2-functionalized glass substrate. A proof-of-concept experiment for the multi-detection of heavy metal ions (Hg(2+) and Cu(2+)) in an aqueous media was also successfully conducted using the dual-functionalized gold islands/glass structure and surface plasmon resonance measurements. The SH groups on the gold islands and the NH2 groups on the glass substrate functioned as spatially separated and selective receptors for Hg(2+) and Cu(2+) ions, respectively. Therefore, both the detection and quantification of Hg(2+) and Cu(2+) ions could be achieved using a single sensing substrate.