In this paper, Golden Ratio Simulated Annealing (GRSA) for Protein Folding Problem (PFP) is presented. GRSA is similar to Multiquenching Annealing (MQA) and Threshold Temperature Simulated Annealing (TTSA) algorithms. In contrast to MQA and TTSA, GRSA uses several strategies in order to reduce the execution time for finding the best solution of PFP. Firstly, temperature parameters are tuned with an analytical-experimental approach; secondly, a heuristic technique for dividing the search space is implemented. GRSA has a special phase which detects the thermal equilibrium by a least squares method. In addition, a reheat strategy to escape from local optima is applied.