The invention provides F-Yb doped quartz core-rod glass with high uniformity and low refractive index and a preparation method thereof. According to the invention, directed at the problem of longitudinal nonuniformity due to serious volatilization of F in Al-Yb doped quartz core-rod glass, and based on an original sol-gel technology for preparation of rare earth doped quartz glass, a hydrothermalmethod and a vacuum freeze-drying technology are introduced into the process of sol-gel preparation for rare earth doped quartz powder, and a co-doping agent P2O5 with a certain content is introduced,so a series of novel Al-P-F-Yb doped quartz glass components different from conventional reported components are developed; a novel glass component formation area is formed; the doping uniformity, specifically the longitudinal uniformity of prepared F-contained quartz glass is greatly improved; meanwhile, the refractive index of the glass is greatly reduced and approximates to the refractive index of pure quartz. The doped quartz glass provided by the invention is used as a core rod of large-mode-area fiber to prepare Yb doped quartz fiber with large mode area and low numerical aperture (NA),so quasi-monomode laser output is obtained.