In this paper, based on non-negative matrix factorization (NMF), we analyzed the ionosphere magnetic field data of the Swarm Alpha satellite before the 2016 (Mw = 7. 8) Ecuador earthquake (April 16, 0.35°N, 79.93°W), including the whole data collected under quiet and disturbed geomagnetic conditions. The data from each track were decomposed into basis features and their corresponding weights. We found that the energy and entropy of one of the weight components were more concentrated inside the earthquake-sensitive area, which meant that this weight component was more likely to reflect the activity inside the earthquake-sensitive area. We focused on this weight component and used five times the root mean square (RMS) to extract the anomalies. We found that for this weight component, the cumulative number of tracks, which had anomalies inside the earthquake-sensitive area, showed accelerated growth before the Ecuador earthquake and recovered to linear growth after the earthquake. To verify that the accelerated cumulative anomaly was possibly associated with the earthquake, we excluded the influence of the geomagnetic activity and plasma bubble. Through the random earthquake study and low-seismicity period study, we found that the accelerated cumulative anomaly was not obtained by chance. Moreover, we observed that the cumulative Benioff strain S, which reflected the lithosphere activity, had acceleration behavior similar to the accelerated cumulative anomaly of the ionosphere magnetic field, which suggested that the anomaly that we obtained was possibly associated with the Ecuador earthquake and could be described by one of the Lithosphere–Atmosphere–Ionosphere Coupling (LAIC) models.