In this paper, a method for making 3D polydimethylsiloxane (PDMS)microfluidic chips with a modified open-source 3D wax printer is demonstrated. The wax was generated with a glass nozzle and a lead zirconate titanate (PZT) actuator. The influence of 3D printing parameters including the degree of overlap and the filling distance between the filling paths on the wax mold were studied. Some typical 3D wax molds such as a 3D shell structure, a 3D letter “U” and a 3D bridge were prepared. Also fabricated were key, functional 3D microfluidic devices including a basket-weave network, a 3D chaotic passive mixer, and a microdroplet generator. True 3D network microflowing was accomplished. This method offers a simple, low-cost way to make 3D microfluidic chips in a short time without clean-room facilities.