High-accuracy measurements and analysis of refractive index change induced by photodarkening and thermal bleaching in ytterbium-doped fibers are presented, based on a modal interference method. Photodarkening-induced refractive index change is positive at the ytterbium lasing wavelengths near $1080\mathrm{nm}$ , and it approaches a saturated level, which is in the order of ${10}^{-6}\sim {10}^{-5}$ for the tested fiber samples. It is found that the value of this refractive index change is linearly proportional to the photodarkening-induced excess loss at an arbitrary probe wavelength in the visible band. Thermal bleaching can only partially erase the photodarkening-induced refractive index change, leaving a residual index change of $(0.2\sim 0.3)\times {10}^{-5}$ . The influence of the photodarkening-induced refractive index change on fiber lasers is discussed.