The invention discloses a protein structure class prediction method based on weighted composition position vectors and a support vector machine. Firstly, protein structure class normal data sets are selected or established, weighting factors are introduced based on composition position vectors, and to-be-predicted protein sequences are represented through the weighted composition position vectors; the weighted composition position vectors are combined with the support vector machine, and the protein structure class prediction method is established through a direct multiclass classification strategy. According to the method, information of amino acid compositions is contained, position information of each amino acid residue in the protein sequences is also contained, the one-to-one correspondence function relation is formed between the position information and the protein sequences, the weighting factors are introduced to the composition position vector representation method, and prediction accuracy can be obviously improved by means of adjusting the weighting factors. The method is simple, rapid and sensitive, and is expected to be applied to other protein prediction fields.