Complex dynamical changes in the ionosphere and thermosphere during geomagnetic storm times could have a significant impact on our communication and navigation applications, as well as satellite orbit determination and prediction activities. Because of the complex electrodynamics coupling processes during storms, which cannot be fully described with the sparse set of thermosphere-ionosphere (TI) observations, it is crucial to accurately model the state of the TI system. The approximation closest to the true state can be obtained by assimilating relevant measurements into physics-based models. Thermospheric mass density (TMD) derived from satellite measurements is ideal to improve the thermosphere through data assimilation. Given the coupled nature of the TI system, the changes in the thermosphere will also influence the ionosphere state. This study presents for the first time a quantification of the changes and improvement of the model state produced by assimilating TMD not only for the thermosphere density but also for the ionosphere electron density. TMD estimates derived from a single Swarm satellite and the Coupled Thermosphere Ionosphere Plasmasphere electrodynamics (CTIPe) physics-based model are used for the data assimilation. The results are presented for a case study during the St. Patrick’s Day storm 2015. It is shown that the TMD data assimilation generates an improvement of the model's thermosphere density of up to 40% (measured along the orbit of the non-assimilated Swarm satellites). The model's electron density during the course of the storm has been improved by approximately 8 and 22% relative to Swarm-A and GRACE, respectively. The comparison of the model's global electron density against a high-quality 3D electron density model, generated through assimilation of total electron content, shows that TMD assimilation modifies the model's ionosphere state positively and negatively during storm time. The major improvement area are the mid-low latitudes. The largest improvements are measured during the storm's recovery phase.