To study the risk of thermal injury in photodynamic therapy for choroidal neovascularization by calculating the retinal temperature of rabbits, a mathematical model for laser induced thermal effect on retina was developed. Homogeneous layer retinal models of different pigmented rabbits were presented to analyze the light distribution. The finite element method realized by Matlab software was used to solve classical bio-heat transfer model - Pennis equation, in which heat loss due to choroidal blood flow was considered. The retinal temperature was calculated with different laser parameters, including different wavelengths (532nm, 578nm and 690nm), power density (200~1600 mW/cm2), spot diameter (1mm, 2mm and 3mm) and different pigmented eye fundi. The prediction results showed the retinal temperature increased first, then reached maximum in a few seconds and kept constant during laser irradiation. Once laser exposure ended, the temperature decreased quickly to normal. With the increase of laser power density and spot size, the retinal temperature raised too. The temperature reduced exponentially with the distance from laser spot increased. The maximum temperature of non-pigmented rabbits was lower than that of pigmented rabbits. The temperature induced by 578nm laser irradiation was highest, the next was by 532nm laser and the lowest was by 690nm laser. For current parameters used to treat choroidal neovascularization (690nm, 600mW, 2mm, 83sec), the maximum retinal temperature calculated was less than 45 °C, which indicating no thermal damage induced.