Manganese dioxides (MnO2) govern the polymerization of phenolic and anilinic pollutants in nature water body. The studies on the chemistry of different phases of MnO2 was relatively limited. Here we compared two MnO2, layer delta-MnO2 and tunnel gamma-MnO2, on their reaction kinetics and removal pathways with acetaminophen (APAP) as model compound. We found the kinetics of acetaminophen transformation by MnO2 were largely influenced by pH values and MnO2 structures. In neutral systems, APAP removal by delta-MnO2 was faster than by gamma-MnO2. This was attributed to the higher catalytic potential of delta-MnO2. In acidic systems, APAP removal by gamma-MnO2 was faster than by delta-MnO2. This was attributed to the larger surface area and weaker electrostatic repulsion of gamma-MnO2 to APAP in acidic conditions. Furthermore, the pathways of acetaminophen transformation were influenced by pH values. Dimerization and hydrolysis-oxidation were the two major APAP transformation pathways by both MnO2 in neutral and acidic systems. Low pH values induced the nucleophilic addition between quinoneimine (the product of hydrolysis-oxidation) and anilines (e.g., APAP and its dimers). Low pH values also promoted the dimerization degrees of APAP. The hydrophilicity of APAP transformation products by MnO2 were significantly reduced by low pH values. This work reconsidered the significances of acidity in the pollutants transformation by MnO2, and provided new perspectives to study the pollutants transformation by different phases of MnO2.