The accumulated heat of light emitted diode (LED) microarray chip at work will result in an excessive junction temperature, which causes a series of adverse effects on the LED microarray chip, severely reduce the reliability of LED microarray chip and even cause permanent damage. Heat dissipation is a key factor that restricts the improvement of working performance of LED microarray, making it an urgent problem to be solved in the manufacturing process of LED microarray chip. A finite element model of AlGaInP-based LED microarray has been built, and the way of modeling, meshing and applying of the boundary conditions has been introduced. Temperature distributions have been analyzed respectively when a single unit and 3×3 units are driven by a pulse current. In order to improve the heat dissipation performance of LED microarray, a structure of heatsink has been designed, the influence of the heatsink on temperature distribution of microarray has been analyzed.