In recent years, typical organic pollutants were frequently found in aquatic environments. Among them, synthetic dyes were widely used in many industries, which resulting in a large amount of wastewater contained dyes. Because of the characteristic of complex components, poor biodegradability and high toxicity, this kind of wastewater brought lots of harm to the ecological environment and organism. In this study, three different types of manganese dioxide (MnO2) with the rod-like, needle-like and mixed morphologies respectively were successfully fabricated by hydrothermal method with changing the preparation conditions and addition of the metal ions, and utilized as activator of persulfate (PS) to remove the dyes aqueous. Subsequently, these MnO2 nanocomposite was characterized by X-ray diffraction (XRD) and scanning electron microscope (SEM) measurements. In addition, Rhodamine B (Rh B), as a representative substance of xanthene dyes was chosen as the target degradants to researched and compared the efficiency of removal via PS activated by different MnO2. By exploring the influences of different reaction parameters on the result of removal, results indicated that PS activated by the acicular MnO2 (α-MnO2) can remove 97.41% of Rh B over 60 min, with the optimal catalyst/PS ratio of 2:1 (the concentration of the α-MnO2 and PS were 1.2 g/L and 0.6 g/L, respectively), pH value of 3, at the temperature of 20 °C. Meanwhile, the probable degradation mechanism was also proposed. At last, as the catalyst was reused for four times, the degradation rate of target degradants decreased less than 10%.