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Background: The regularity study of protein molecular evolution is the key to molecular evolution and it has important meaning to reveal life origin and the evolutionary mechanism.TIM-barrel fold is a typical fold type and members of this fold have a common topology but with little sequence similarity through evolution.The pairwise amino acid sequence diversity of TIM-barrel fold proteins can be up to 70%, so it is difficult to detect their evolutionary relationship from sequence.As a result of the growing number of protein structure information of PDB and the development of structure alignment algorithms, basing on structure comparison make it better to study TIM-barrel fold proteins than that of sequence.Methods: In this paper, 326 TIM-barrel proteins with the spatial structure material and known species information were selected from Astral 1.65 (sequence identity <95%) as different level datasets.TIM-barrel protein dataset, alpha-amylase subset, triosephosphate isomerase subset, and D-xylose isomerase subset were established to construct clustering dendrograms using their structure alignment information, respectively.The species phylogenies of different datasets were obtained from NCBI.Results: The analysis about clustering dendrograms of TIM-barrel protein dataset shows that proteins with similar function obviously tend to cluster.The same superfamily members are almost clustered in a large branch and the same family members are clustered in a small branch belonging to their superfamilys.However, there is little relation between clustering dendrograms and their corresponding species phylogenies.The analysis of other three subsets indicates that under the constraints of function, clustering dendrograms of TIM-barrel proteins have a good corresponding relation with species phylogenies.Conclusions: Our results indicate that the structure evolution of TIM-barrel proteins reflects the constraints of protein function, the structural differences between specific functional TIM-barrel proteins show species specificity.The structure evolution implies the evolution information of species .