This paper established an optimized algorithm for temperature field distribution of rat brain tissue undergoing radio frequency ablation (RFA) treatment. Firstly, adopting the Pennes bio-heat transfer equation, obtained the temperature distribution of rat brain tissue with different RFA temperature and duration by using the finite element analysis software FEMLAB (COMSOL). Then, obtained the optimized algorithm of temperature field distribution of biological tissue undergoing RFA treatment by extracting and analyzing the temperatures at different positions using MATLAB6.5 and the fitting software 1stOpt. Finally, model validation was carried out with FEMLAB simulations. Results show that the optimized algorithm of temperature field distribution established in this paper is feasible. According to the optimized algorithm, it is convenient, fast, accurate and real-time to obtain the instantaneous temperature at any position of the rat with any RFA temperature and duration.