A new polymer microlens with variable focusing properties is designed and fabricated. The microlens consists of a thin diaphragm with 3D convex lens, chamber and microchannel, which are made of polydimethyl-siloxane (PDMS). A novel fabrication approach has been developed to cast the PDMS microlens film using a PDMS mold. The elastomeric PDMS microlens film acts as a diaphragm. The flexible PDMS microlens and diaphragm are integrated on a microfluidic chip. By varying the pressure in the microfluidic chamber, which produces a shift in the microlens' focal plane, this can change the back focal length of lens. The new fabrication method provides easy fabrication, low-cost production and precise dimension control. Measurement with an atomic force microscope reveals that the surface roughness of the lens is 18.6 nm, and real-time contact-angle measurements show the back focus length tuning range is from 3.8 mm to 10.6 mm. The variable focal length of the microlens is critical to increase the efficiency of the light detection in optical or biophotonic applications. In this paper, the fabrication processing, mechanical and optical property testing, and simulation results are presented in detail.