The one-dimensional fluid/kinetic code TRANSCAR is used to simulate the effects of geomagnetic activity on the atomic oxygen (3P-1D) red and (1D-1S) green thermospheric dayglows at 630.0 and 557.7 nm, associated with the modification of the density structure of the neutral atmosphere. It is found that when magnetic activity increases from quiet to strong, the altitude of the peak of both emissions increases by <10%, the peak intensity of the 557.7 nm thermospheric layer decreases by about 40%, and the peak intensity of the 630.0 nm layer remains almost constant. The prevailing production and quenching processes are reviewed and their variations are explained in terms of changes in the ionospheric and thermospheric parameters which are induced by the rise of the geomagnetic activity. Together with this model study a 4-year set of WINDII data is analyzed. The measurements confirm the trends previously revealed by the TRANSCAR model. No statistical variation of the 630.0 nm peak emission is seen, while the anticorrelation between the 557.7 nm thermospheric peak intensity and the magnetic activity is clearly found.