Laser micro-welding is widely used for the manufacturing process in the electrical and the electronics industries, where the demands for the miniaturization, the high strength and the temperature resistance are constantly increasing. Recently, a flexible printed circuit (FPC) is expected as a new connection technology between electrical conductors according to the improvement of reliability and controllability with the diversification of the design concept. In this technology, it is required to weld a several tens μm thickness of FPC and a several hundreds μm thickness of metal electrode. This material combination accompanies the difficulty to control the welding due to the difference of thermal properties and heat capacity. In this study, the overlap welding of thin copper circuit on a polyimide film and a thick brass electrode was experimentally and numerically investigated by using a pulsed Nd:YAG laser, and a shearing stress of overlap welding was evaluated with and without the control of pulse waveform, which can achieve various heat input configurations. The results showed that the porosity was observed as the major weld defect in the welding process without a pulse control. However, the appropriate controlled laser pulse configuration of micro-welding could remove the welding defects in the molten area, improve the weld penetration stability and increase the weld strength. The potential benefits of pulse waveform were discussed for the direct laser micro-welding process. It is clarified that the direct laser micro-welding of a thin copper circuit on a polyimide film and a thick brass electrode could be realized by using a proper control of laser pulse and heat input.