We reports a detailed study on a novel design of a Joule-heating-induced polymerase chain reaction (PCR) microchip directly heated by applying electric current to the ends of the geometric varied microchannel, which is simulated together with the factors acting on the temperature distribution. Treating the continuous flowing fluid in the channel as the resistance, different channel shapes would lead to the different resistances, which generates various heat when the fixed current is applied to the ends of channel. Based on the Ohm’s law and the Joule-Thomson effect, three required sequential temperature zones are obtained. The temperature cycling is achieved and the factors that contribute to the temperature distribution are simulated and analyzed, such as the environment temperature, the heat transfer coefficient, the current density, the fluid velocity, and the channel shape. The design of the Joule-heating-induced PCR microchip sheds light on the future novel application of continuous-flow PCR. By applying certain conditions, thermal cycles that meet PCR requirements can be achieved.