Yb3+:YAl3(BO3)4 crystals were grown in Li2WO4–B2O3 and K2Mo3O10–B2O3 fluxes, respectively. In the same experimental conditions, a shorter ultraviolet absorption edge of 278 nm, longer fluorescence lifetime of 1.1 ms, higher slope efficiency of 58%, and lower threshold of 2.4 W were obtained in a Yb3+:YAl3(BO3)4 crystal grown in Li2WO4–B2O3 flux, whereas the corresponding values for the crystal grown in K2Mo3O10–B2O3 traditional flux were 318 nm, 0.7 ms, 46%, and 3.1 W, respectively. Therefore, spectroscopic and laser performances of the one grown in Li2WO4–B2O3 flux are enhanced due to the improved crystal optical quality.