The invention discloses an Yb-doped fiber and a manufacturing method thereof. The Yb-doped fiber comprises a core layer at least containing Yb and Al, a glass matrix cladding surrounding the core layer, and a low-refractive index coating layer surrounding the glass matrix cladding. The glass matrix cladding comprises an inner cladding and an outer cladding. The refractive index of the inner cladding is lower than that of the core layer, and higher than that of the outer cladding. The inner cladding uses Ge, P, Al, and F as doping agents. The core layer is doped with F and P as doping agents. A MCVD method is used to manufacture a performing bar, fiber-drawing temperature is controlled, so optical fibers are drawn under relatively low tension, and required fibers are obtained. Through improving the refractive index of the inner cladding, relatively through reducing the difference between the refractive index of the core layer and the refractive index of the inner cladding, relatively high Al and Yb doping concentration in a fiber core is maintained, so as to reduce core layer NA under the condition that relatively high fiber cladding absorption coefficient is maintained, and single-mode output is realized, that is, fiber quality factor is proximity to one. The manufacturing method can manufacture a high-concentration Yb-doped fiber, and realizes relatively high cladding absorption coefficient.