The invention relates to a protein remote homology detecting method and device. The method comprises a training process and a detecting process. The training process comprises the steps that protein samples are regarded as an inquiring sequence and input into a set of protein homology detection bases based on ranking strategies to be ranked, retrieval is conducted in a database, each retrieval result corresponds to a homology similarity grade, all the retrieval results are ranked in a descending mode and combined into characteristic vectors, the obtained characteristic vectors are input into a method based on ranking study to be trained, and a ranking model is obtained. The detecting process comprises the steps that characteristic vectors of target protein are obtained in the mode similar to that of the training process, the characteristic vectors are input into the trained ranking model to be ranked, a ranking result is obtained, and the remote homology detecting result of the target protein is determined according to the ranking result. According to the protein remote homology detecting method and device, the ranking detecting results of the multiple bases are combined, then the ranking studying method is used for conducting training to obtain the ranking model, and thus the detecting accuracy and stability can be effectively improved.