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We report transport studies on magnetically doped topological insulator ultrathin films grown by molecular beam epitaxy. The magnetotransport behavior exhibits a systematic crossover between weak antilocalization and weak localization with the change of magnetic impurity concentration, temperature, and magnetic field. We show that the localization property is closely related to the magnetization of the sample, and the complex crossover is due to the transformation of from a topological insulator to a topologically trivial dilute magnetic semiconductor driven by magnetic impurities. This work demonstrates an effective way to manipulate the quantum transport properties of the topological insulators by breaking time-reversal symmetry.