The invention provides a self-adaptive filtering method for data of a pipeline magnetic flux leakage inner detector, and relates to the technical field of fault diagnosis techniques of pipelines. The method comprises the following steps that magnetic flux leakage signals are acquired by the pipeline inner detector, are amplified and stored, and are transformed into the actual digital voltage signals, the digital voltage signals are subjected to baseline correction, and then the abnormal data are searched, eliminated and compensated; the single-channel signal classification are conducted, and different types of signals are subjected to line filtering through corresponding single-channel self-adaptive filtering algorithms; the influence degree of noises between the adjacent channels is compared and analyzed to implement multi-channel equalization on the magnetic flux leakage signals; and the multi-channel signal area classification is conducted, and the different signal areas are subjected to surface filtering through corresponding multi-channel self-adaptive filtering algorithms. According to the method provided by the invention, the predication of the service life of the pipeline is more accurate, the feature is much easier to extract in the fault diagnosis of the pipeline, the filtering effect is more obvious, and the function of rapidly and accurately processing big data is achieved.