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A 3 × 3 tunnel-structured manganese oxide, todorokite, or MnO6 octahedral molecular sieve (OMS-1), was synthesized at atmospheric pressure by a refluxing process from birnessite, the layer-structured precursor. The todorokite synthesized by the refluxing process (named as OMS-1-R) consisted of fibers with various lengths and platy trilling patterns, made of fiber crystals twinned with each other at 120°, from which the fibers matted and extended. Intergrowth of different widths of tunnels commonly occurred in a disorderly manner, with a triple octahedral chain width being the most predominant. Such morphological and intergrowth characteristics were similar to those of natural todorokites and a hydrothermally synthesized todorokite. When refluxing time was increased, the crystallinity of OMS-1-R was promoted and small scale twinning in morphology became a relatively large and coarse twinning. However, there was no other crystalline phase produced. The OMS-1-R24, synthesized after 24 h of refluxing, with a chemical composition of Mg0.17MnO2.10(H2O)0.88, was stable up to 400 °C. The BET surface area was found to be 77 m2/g, and the surface was predominantly mesoporous with the BJH adsorption average pore diameter of 14 nm.