The invention provides a method and device for detecting single sample body cell mutation sites in abnormal tissue and a storage medium. The method includes the following steps that the effective sequencing sequence of an abnormal sample and the effective sequencing sequence of a simulated normal sample are obtained; in the effective sequencing sequences, basic groups, different from basic groups of the simulated normal sample, of the abnormal sample are obtained, according to the mutation basic group frequency, the types of the basic groups of the abnormal sample and the simulated normal sample are judged, the FISHER is then used for accurately detecting the difference of the types of the basic groups, and according to the difference, the mutation type is judged; by filtering the mutation types, false positive mutation and germ cell mutation are removed, and high-reliability somatic cell mutation sites are obtained. The method has the advantages of being high in sensitivity and specificity, has high sensitivity in mutation detection of known mutation genes, and new mutation genes can be found.