To estimate the risks and developing remediation strategies for the mercury (Hg)-contaminated soils, it is crucial to understand the mechanisms of Hg transformation and migration in the redox-changing paddy fields. In present study, a Hg-spiked acidic paddy soil (pH 4.52) was incubated under anoxic conditions for 40 d and then under oxic conditions for 20 d. During anoxic incubation, the water-soluble, exchangeable, specifically adsorbed, and fulvic acid-complexed Hg decreased sharply, whereas the humic acid-complexed Hg, organic, and sulfide-bound Hg gradually increased, which were mainly ascribed to the enhanced adsorption on the surface of soil minerals with an increase in soil pH, complexation by organic matters, precipitation as HgS, and absorption by soil colloids triggered by reductive dissolution of Fe(III) oxides. By contrast, after oxygen was introduced into the system, a gradual increase in available Hg occurred with decreasing soil pH, decomposition of organic matters and formation of Fe(III) oxides. A kinetic model was established based on the key elementary reactions to quantitatively estimate transformation processes of Hg fractions. The model matched well with the modified Tessier sequential extraction data, and suggested that large molecular organic matter and humic acid dominated Hg complexation and immobilization in acidic paddy soils. The content of methylmercury increased and reached its peak on anoxic 20 d. Sulfate-reducing bacteria Desulfovibrio and Desulfomicrobium were the major Hg methylating bacteria in the anoxic stage whereas demethylating microorganisms Clostridium_sensu_stricto_1 and Clostridium_sensu_stricto_12 began to grow after oxygen was introduced. These new dynamic results provided new insights into the exogenous Hg transformation processes and the model could be used to predict Hg availability in periodically flooded acidic paddy fields.