In order to study the thermal and stress fields in the multilayered structure of silicon-based positive-intrinsic-negative(PIN) photodiode irradiated by millisecond(ms)-pulsed laser, we use the thermal elasto-plastic constitutive theory and the equivalent specific heat method, to deal with the phase change latent heat. The multiple-heat-source, especially the influence of reflection from bottom-aluminum-electrode, and the effect of the nonlinearity of material parameters are taken into consideration. A 2-D simulation model is built by means of the finite element simulation software of COMSOL Multiphysics. The surface and the internal each layer showing changes of the transient distribution and evolution of the thermal and stress fields with space and time can be obtained. Because of taking account of the reflection of the aluminum electrode, the temperature of the aluminum electrode rises slightly. On this basis, we analyze the hard failure mechanism of ms-pulsed laser irradiated silicon-based PIN, and the mechanical damage before melting that leads to a malfunction of silicon-based PIN detector.