Manganese (Mn) has the potential to reduce cadmium (Cd) uptake by rice; however, the efficiency depends on its soil availability. Therefore, this study designed a slow-release Mn fertilizer by employing a polyacrylate coating. Pot trials were conducted to study the effects of coated-Mn and uncoated-Mn alone or in combination with lime on the dynamics of soil dissolved-Mn and available Cd, and the transportation of Mn and Cd within rice. The results showed that coated-Mn declined the release of Mn until the 7th day of application; however, it consistently supplied more dissolved-Mn than uncoated-Mn. As a result, coated-Mn induced a greater Cd reduction (45.8%) in brown rice than uncoated-Mn (9.7%). The total Cd of rice and its proportion in brown rice were greatly reduced by coated-Mn, indicating the inhibition of root uptake and interior transport of Cd. Additionally, lime addition prominently increased the soil pH and decreased the CaCl2-extractable Cd (90.1–93.9%). However, since lime reduced the soil dissolved-Mn, downregulated the OsHMA3 expression and upregulated the OsNramp5 expression, brown rice Cd was reduced by only 43.0%. The combined addition of lime and coated-Mn alleviated the liming effect on soil Mn and gene expression in roots, thereby reducing brown rice Cd by 71.5%.