The classification of protein structures is essential for their function determination in bioinformatics. The success of the protein structure classification depends on two factors: the computational methods used and the features selected. In this paper, we use a combinatorial fusion analysis technique to facilitate feature selection and combination for improving predictive accuracy in protein structure classification. When applying these criteria to our previous work, the resulting classification has an overall prediction accuracy rate of 87% for four classes and 69.6% for 27 folding categories. These rates are significantly higher than our previous work and demonstrate that combinatorial fusion is a valuable method for protein structure classification.