Yb3+/Al3+ co-doped silica fibers (YDFs) with almost identical core glass compositions were prepared using the sol-gel and modified chemical vapor deposition (MCVD) methods. The photodarkening (PD) and laser performance before and after the PD process were tested under 974 nm pumping. The doping homogeneity of Yb3+ ions and clusters of Yb3+ ions in preform slices of these two fibers were investigated via optical absorption spectroscopy, photoluminescence emission spectra, electron probe microanalysis (EPMA), and low-temperature (4 K) electron paramagnetic resonance (EPR). It is known that the PD resistance of YDFs prepared via the sol-gel method is significantly better than that of YDFs prepared via MCVD under the same test conditions. EPMA mapping reveals that the doping homogeneity of Yb3+ ions in the sol-gel fiber core glass is better than that in the MCVD fiber. The low-temperature (4 K) EPR and cooperative luminescence spectra of Yb3+ ions indicate that the clustering degree of Yb3+ ions in the sol-gel fiber is lower than that in the MCVD fiber. In the absorption and emission spectra, small amounts of Yb2+ ions are observed in the preform slice from the sol-gel method. A model of the color-center generation in the PD process was proposed to explain the mechanism of PD resistance improvement for the YDFs fabricated via the sol-gel method.