A novel low-cost molding process to prepare polymer-based micro-lens arrays with spacers for optical applications was investigated in this paper. The process consists of the following steps: 1) hemispherical glass bubble arrays, used as the upper part of the molds, was prepared by combining a hot-forming process and a chemical-foaming process; 2) the silicon mold, used as the lower part of the molds, was fabricated by etching; 3) an anti-stick layer was coated on the concave surface of the glass mold; and 4) the lens material, UV-curable glue, was dispensed into the concave molds, followed by curing and de-molding. The optical properties of the lens were characterized by a profile meter and a beam analyzer. The results showed that the micro-polymer lens arrays with spacers were successfully prepared using the low-cost wafer-level glass-silicon mold. The results indicate that the micro-lenses have hemispherical structures and smooth surface.