This paper describes the density correction of the NRLMSISE-00 using more than 15 years (2002–2016) of TIMED/SABER satellite atmospheric density data from the middle atmosphere (20–100 km). A bias correction factor dataset is established based on the density differences between the TIMED/SABER data and NRLMSISE-00. Seven height nodes are set in the range between 20 and 100 km. The different scale oscillations of the correction factor are separated at each height node, and the spherical harmonic function is used to fit the coefficients of the different timescale oscillations to obtain a spatiotemporal function at each height node. Cubic spline interpolation is used to obtain the correction factor at other non-node heights. The spatiotemporal correction function depends on six key parameters, including height, latitude, longitude, local time, day, and year. The evaluation results show that the spatiotemporal correction function proposed in this paper achieves a good correction effect on the atmospheric density of NRLMSISE-00. The correction effect becomes more pronounced as the height increases. After correction, the relative error of the model decreased by 40%–50% in July, especially at ±40° N in the 80–100 km region. The correction effect of the spatiotemporal correction function under different geomagnetic activity may have some potential relationships with geomagnetic activities. During geomagnetic storms, the relative errors in atmospheric density at 100, 70, and 32 km decrease from 41.21%, 22.09%, and 3.03% to −9.65%, 2.60%, and 1.44%, respectively, after correction. The relative errors in atmospheric density at 100, 70, and 32 km decrease from 68.95%, 21.02%, and 3.56% to 3.49%, 2.20%, and 1.77%, respectively, during the geomagnetic quiet period. The correction effect during the geomagnetic quiet period is better than that during geomagnetic storms at a height of 100 km. The subsequent effects of geomagnetic activity will be considered, and the atmospheric density during magnetic storms and quiet periods will be corrected separately near 100 km. The ability of the model to characterize the mid-atmosphere (20–100 km) is significantly improved compared with the pre-correction performance. As a result, the corrected NRLMSISE-00 can provide more reliable atmospheric density data for scientific researches and engineering fields, such as data analysis, instrument design, and aerospace vehicles.