This paper describes a novel finite element thermal analysis model for an AlGaInP-LED micro-array device. We also conduct a transient analysis for the internal temperature field distribution of a 5×5 array device when a 3×3 unit is driven by pulse current. In addition, for broader applications, a simplified thermal analysis model is introduced and its accuracy is verified. The internal temperature field distribution of 100×100 units is calculated using the simplified model. The temperature at the device center reaches 360.6 °C after 1.5 s. In order to solve the heat dissipation problem of the device, an optimized heat dissipation structure is designed, and the effects of the number and size of the heat dissipation fins on the thermal characteristics of the device are analyzed.