A non-negative tensor decomposition (NTD) approach has been developed to analyze the ionospheric magnetic field data of the Swarm Alpha and Charlie satellites for the Mw7.8 2015 Nepal earthquake. All available satellite data were analyzed regardless of geomagnetic activity. We used the amplitude time-frequency spectra of the two-satellite data to build third-order tensors and decomposed them into three components. One of these components seems to be more affected by seismicity. In particular, the cumulative number of anomalous tracks of this component displays accelerated growth that conforms to a Sigmoid fit from 60 to 40 days before the mainshock. Subsequently, until 10 days before the earthquake, it shows a weak accelerating trend that obeys a power-law behavior and then resumes linear growth after the mainshock. Moreover, the cumulative anomaly was indicated not to be caused by geomagnetic activity, solar activity or other non-seismic factors. An investigation of the foreshocks around the epicenter reveals that the cumulative Benioff strain also exhibited two accelerated growths before the mainshock, which is consistent with the cumulative result of ionospheric anomalies. In the first acceleration stage, seismicity appeared in the region surrounding the epicenter, and most of the ionospheric anomalies were offset away from the epicenter. During the second acceleration stage, some foreshocks occurred closer to or on the mainshock fault, and ionospheric anomalies also appeared near two faults around the epicenter. Furthermore, the correspondence between the ionospheric anomalies and the anomalies in different geo-layers can be explained by the lithosphere–atmosphere–ionosphere coupling model.