Abstract Geomorphologies and mechanisms of thermospheric mass density variations caused by geomagnetic storms are still challenging due to limited observations and imprecise models. Recently, precise orbit determination (POD) of Gravity Recovery and Climate Experiment (GRACE) and Swarm satellites is able to estimate thermospheric mass density variations, which may provide data to study thermospheric mass density variations following the storm. In this paper, the thermospheric mass density is estimated from GRACE-A and Swarm-A POD and the distinct thermospheric mass density variations are investigated as function of latitude during the September 2017 geomagnetic storm. Different enhancements in mass density response to the geomagnetic storm are presented for the Northern (GRACE) and the Southern (Swarm) Hemispheres. Swarm observations show symmetric mass density variations between two hemispheres and a slightly stronger enhancement in Southern Hemisphere. GRACE POD and accelerometer observations both show a very strong enhancement in Northern Hemisphere while no corresponding enhancement in Southern Hemisphere. This anomaly may attribute to the effects of vertical winds in high latitude region and plasma drift considering the similar solar zenith angles in both hemispheres.