In this study, new manganese oxide (i.e., black-birnessite) particles with nanostructures were prepared and its physico-chemical properties and oxidative-transformation efficiency on 1,4-naphthoquinine(1,4-NPQ) in the presence of reactive mediator was investigated. The results were also compared with that of the manganese oxide (i.e., brown-birnessite) particles synthesized by classical McKenzie method. Analysis of XRD and SEM data show that the particles are a single phase corresponding to a birnessite-based manganese oxide with cotton ball-like shapes containing nanofibers. In batch experiments, removals of 1,4-NPQ by the black-birnessite follows pseudo-first-order kinetics and the rate constant values obtained are greater about 2.3 times than that of the brown-birnessite in spite of its lower surface area (41.0 vs 19.80 $m^2/g$). The results can be explained by the higher crystallinity and nano structured features of the back-birnessite particles, which give higher reactivity for the removals of the quinone compound. HPLC analysis of the reaction products confirmed that the balck-birnessites removed 1,4-NPQ through cross-coupling reaction in the presence of catechol as a reactive mediator.