Owing to its effectiveness and being environment-friendly, biochar has been used for adsorbing and immobilizing pollutants in soil in recent years of studies, which is also suitable for manganese pollution in soil caused by manganese mining and processing activities. In this research, alkali-modified pomelo biochar (MBC) was regarded as a soil amendment, and the improvement of soil physicochemical properties and Mn2+ sorption and transport in soil by modifying with MBC were investigated. In incubation experiment, 0–10% (w/w) MBC addition amount significantly improved the physicochemical properties of soil. Due to the amelioration of soil physicochemical properties along with the oxygen-containing functional groups and the developed pore structure of MBC itself, the adsorption capacity of MBC modification soil towards Mn2+ (qe) was enhanced in batch adsorption experiment, and qe increased by 10–108% when MBC ratio grew from 0 to 10% at 300 mg·L−1 Mn2+ solution. In column transport experiment, the Mn2+ retention rate climbed by 13–106% from 0 to 10% MBC addition proportion when adopted the MBC filling way that placed MBC on the soil upper layer, and the reinforced restriction on Mn2+ transport in soil amended with MBC might ascribe to the enhanced qe as well as the reduced saturated hydraulic conductivity. These results proved that MBC effectively augmented adsorption ability and suppressed transport of Mn2+ in soil, which could provide an available mind on prevention and remediation of soil Mn contamination.