The search for low energy states of molecular clusters is associated with the study of molecular conformation and especially protein folding. This paper describes a new global minimization algorithm which is effective and efficient for finding low energy states and hence stable structures of molecular clusters. The algorithm combines simulated annealing with a class of effective energy functions which are transformed from the original energy function based on the theory of renormalization groups. The algorithm converges to low energy states asymptotically and is more efficient than a general simulated annealing method.