This paper presents a novel low-cost poly(dimethylsiloxane) (PDMS) micropump with simple planar design featuring use of compliant in-contact check valves for reliable operation and easy system integration. The micropump mainly consists of two PDMS functional layers: one through-opening layer incorporating the planar in-contact check valves, pump chamber and flow channels, and the other thin membrane layer covering the chamber with a miniature permanent magnet on top for actuation. A special clamping molding technique was used to fabricate the through-opening functional layer, with which the flap-stopper based planar check valve was manipulated to contact each other enabling the minimized leakage flow. The micropump was then characterized by investigating the dependence of pumping flow rate on the driving frequency and backpressure. Testing results exhibit that the micropump is able to produce a flow rate at least of 3.0 μL/min, and work reliably against a backpressure of 1900 Pa, demonstrating the feasibility of this micropump for potential use in various lab-on-a-chip systems.