Highly Yb-doped silica glass with low refractive index for fabrication of Yb-doped large-mode-area photonic crystal fiber (LMA PCF) is in favor of decreasing fiber length and thus increasing the threshold of nonlinear effects in pulse laser amplification. Accordingly, fluorine incorporation in highly Yb-doped silica glass is vitally important to compensate the sharp increase in refractive index caused by ytterbium and aluminum ions. In this work, the fluorine doping concentration in Yb/Al/P/F co-doped silica glass was significantly improved by a modified sol-gel method combined with high temperature sintering. The effects of fluorine doping on glass structure have been investigated in details by Raman spectra, nuclear magnetic resonance (NMR) and advanced pulse electron paramagnetic resonance (EPR) measurements. The incorporation of fluorine yields Si-F bonds and Yb-F bonds formation and leads to the mild change in spectroscopic properties. An optimized silica core glass rod with high Yb (0.77 wt.%) and fluorine (0.8 wt.%) doping concentration, low refractive index and acceptable optical quality was prepared. Based on the highly fluorine and ytterbium doped silica core glass, a polarization maintaining (PM) photonic crystal fiber with 40 µm core was prepared and the pump absorption coefficient at 976 nm was ∼6.5 dB/m. An average amplified power of 103 W was achieved from a 2-m-long PCF with the bend diameter of 23 cm. The slope efficiency (with respect to pump power) was 52% with laser beam quality factor M2 of 1.46.