The thermal properties of modified uni-traveling carrier (MUTC) photodiode flip-chip bonded to AlN and diamond are simulated. The thermal impedance of InGaAs is the primary source of internal heating. An n-down epitaxial structure is designed to improve thermal dissipation. Compared to the conventional p-down configuration, the n-down MUTCs bonded to diamond, or AlN submounts achieved 145% and 110% improvement in dissipated power density at thermal failure, respectively. The improved thermal characteristics presage higher RF output power before thermal failure.