The invention relates to a multi-variation strategy protein structure prediction method combined with evaluation of exclusion degree. The multi-variation strategy protein structure prediction method includes the steps: under an evolution algorithm framework, 1) establishing three different variation strategies, selecting one variation strategy according to a mode of roulette to perform variation on conformation, and performing 3-segment assembling for once time on the generated variation conformation to generate a variation conformation; 2) performing crossed operation on the variation conformation; and 3) using a Rosetta energy function score3 and a Monte Carlo Boltzmann acceptance criteria to select the conformation with the index {1, 2, ..., NP/2}, and using an exclusion index Exclusion, and the Monte Carlo Boltzmann acceptance criteria for selecting the conformation with the index {(NP/2)+1, (NP/2)+2,..., NP}. The multi-variation strategy protein structure prediction method combined with evaluation of exclusion degree can increase the diversity of populations, and can alleviate the problem that the energy function is not accurate, thus improving the sampling efficiency. The multi-variation strategy protein structure prediction method combined with evaluation of exclusion degree has high sampling efficiency and high prediction accuracy.