Laser induced graphene technology on a polyimide (PI) film substrate for supercapacitors, flexible sensors and heaters, has been a hot topic due to its fast fabrication speed and 3D controllable microstructure formation. However, the thin PI film will suffer burnthrough of the film under the required high energy density to form graphene. Herein, we introduced an auxiliary cooling semiconductor plate beneath the PI substrate to decrease the temperature of the substrate to reduce the burnt thickness. Experiment results showed that the burnt thickness will decrease to about 33.39 µm for −2°C on the thin film with thickness about 12 µm and the value of resistance can still be kept at 8.33 k Ω. The effects of the scanning speed and power on the size of the wire also discussed. Therefore, such method may open a way to fabricate graphene patterns on thin films with thickness less than a few micrometers, which will play an important role in applications including electronic skins and multi-layer flexible plastic circuits.