We present a detailed spectral analysis of the brightest Active Galactic Nuclei (AGN) identified in the 7Ms Chandra Deep Field South (CDF-S) survey over a time span of 16 years. Using a model of an intrinsically absorbed power-law plus reflection, with possible soft excess and narrow Fe K$alpha$ line, we perform a systematic X-ray spectral analysis, both on the total 7Ms exposure and in four different periods with lengths of 2-21 months. With this approach, we not only present the power-law slopes, column densities $N_H$, observed fluxes, and absorption-corrected 2-10~keV luminosities $L_X$ for our sample of AGNs, but also identify significant spectral variabilities among them on time scales of years. We find that the $N_H$ variabilities can be ascribed to two different types of mechanisms, either flux-driven or flux-independent. We also find that the correlation between the narrow Fe line EW and $N_H$ can be well explained by the continuum suppression with increasing $N_H$. Accounting for the sample incompleteness and bias, we measure the intrinsic distribution of $N_H$ for the CDF-S AGN population and present re-selected subsamples which are complete with respect to $N_H$. The $N_H$-complete subsamples enable us to decouple the dependences of $N_H$ on $L_X$ and on redshift. Combining our data with that from C-COSMOS, we confirm the anti-correlation between the average $N_H$ and $L_X$ of AGN, and find a significant increase of the AGN obscured fraction with redshift at any luminosity. The obscured fraction can be described as $f_{obscured}thickapprox 0.42 (1+z)^{0.60}$.
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