Positive-intrinsic-negative (PIN) limiter are widely used to protect sensitive components from leakage power itself and adjacent high-power injection. Being the core of a PIN limiter, the PIN diode is possible to be burnt out by the external microwave pulses. Here, numerical simulations by our self-designed device-circuit joint simulator were carried out to study the influences of the I layer thickness and the anode diameter of the PIN diode on the maximum temperature variation curve of the PIN diode limiter. The damage threshold criterion in the numerical simulation was first studied by comparing experimental results with simulation results. Then, we determined the impact of the structure on the thermal burnout effect induced by microwave pulses of PIN limiter diodes.