The important factors in secondary structures of mRNA influencing on protein folding rates are found during our previous research, and there are kinds of complex loop structures in secondary structures of mRNA. Do these complex loop structures have important influences on protein folding rate? Do different loop structures have similar effects on protein folding rate? Based on this idea, a data set that contains both the information of internal loops, hairpin loops, bulge loops, multi-branch loops and protein folding rates was constructed. For each protein in the data set, the secondary structures of mRNA were predicted followed by calculations of the parameters of mRNA secondary structures, including the base content of each loop structure, the content of base pairs, and the base content of the single strand. Analyses of the relationship between the protein folding rates and each parameter of loop structures of mRNA reveal that the protein folding rate has a significant positive correlation with the content of each kind of the four loop structures, it means that the loop structures of mRNA act as a kind of influential factors for the protein folding rate. Given the proteins in the data set were classed into different folding types and different secondary structural types, the relationship analyses reveal that for proteins in different types, the effects of loop structures on protein folding rate are significantly different. This work will provide the theoretical basis for the future study of mRNA and protein folding rate.