We discuss the violation of quark-flavor symmetry at high temperatures, induced from nonperturbative thermal loop corrections and axial anomaly, based on a three-flavor linear-sigma model including an axial-anomaly induced-flavor breaking term. We employ a nonperturbative analysis following the Cornwall-Jackiw-Tomboulis formalism, and show that the model undergoes a chiral crossover with a pseudo-critical temperature, consistently with lattice observations. We find following features regarding the flavor breaking eminent around and above the pseudo-critical temperature: i) up-and down-quark condensates drop faster than the strange quarks toward the criticality, but still keep nonzero value even going far above the critical temperature; ii) the introduced anomaly-related flavor-breaking effect acts as a catalyzer toward the chiral restoration, and reduces the amount of flavor breaking in the up, down and strange quark condensates; iii) a dramatic deformation for the meson flavor mixing structure is observed, in which the anomaly-induced favor breaking is found to be almost irrelevant; iv) the meson spectroscopy gets corrected by the net nonperturbative flavor breaking effects, where the scalar meson mass hierarchy (inverse mass hierarchy) is significantly altered by the presence of the anomaly-related flavor breaking; v) the topological susceptibility significantly gets the contribution from the surviving strange quark condensate, which cannot be dictated by the chiral perturbation theory, and deviates from the dilute instanton gas prediction. There the anomaly-induced flavor breaking plays a role of the destructive interference for the net flavor violation; vi) the U(1)_A breaking is enhanced by the strange quark condensate, which may account for the tension in the effective U(1)_A restoration observed on lattices with two flavors and 2+1 flavors near the chiral limit.