Abstract: A method is disclosed for integrating multi-omics data to extract a microsatellite instability (MSI)-based neoantigen for immunotherapy. The method includes the following steps: S1, integrating DNA and RNA sequencing data of a patient to detect the microsatellite instability (MSI) of the patient accurately; S2, translating open reading frames (ORFs) influenced by the detected MSI to acquire an MSI proteome; S3, mapping the MSI proteome against a normal human proteome to acquire a sample-specific proteome; and S4, acquiring a sample neoantigen. The new method reduces the rate of false positives in MSI detection, which is especially relevant for improving the efficacy of current clinical immunotherapy.