Laser induced morphological damage have been observed in silicon-based positive-intrinsic-negative photodiode. This paper adopted the methods of the theoretical calculation and finite element numerical simulation to model, then solved the temperature field and thermal stress field in silicon-based positive-intrinsic-negative photodiode irradiated by multipulsed millisecond laser, and researched the features and laws of the temperature field and thermal stress field. As for the thermal-mechanical problem of multipulsed millisecond laser irradiating silicon-based positive-intrinsic-negative photodiode, based on Fourier heat conduction and thermoelasticity theories, we established a two-dimensional axisymmetric mathematical model .Then adopted finite element method to simulate the transient temperature field and thermal stress field. The temperature dependences of the material parameters and the absorption coefficient were taken into account in the calculation. The results indicated that there was the heat accumulation effect when multipulsed millisecond laser irradiating silicon-based positive-intrinsic-negative photodiode. The morphological damage threshold were obtained numerically. The evolution of temperature at the central point of the top surface, the temperature distribution along the radial direction in the end of laser irradiation and the temperature distribution along the axial direction in the end of laser irradiation were considered. Meanwhile, the radial stress, hoop stress, axial stress on the top surface and the R=500μm axis were also considered. The results showed that the morphological damage threshold decreased with the increased of the pulse number. The results of this study have reference significance of researching the thermal and thermal stress effect evolution’s features when multipulsed millisecond laser irradiating silicon-based positive-intrinsic-negative photodiode, then revealing the mechanism of interactions between millisecond laser and photodiode.