<p>This study aimed to investigate the cause of susceptibility underestimation in body quantitative susceptibility mapping (QSM) and propose a water/fat separate reconstruction to address this issue. A numerical simulation was conducted using conventional QSM with/without body masking. The conventional method with body masking underestimated the susceptibility across all regions, whereas the method without body masking estimated an equivalent value to the ground truth. Additional numerical simulations and human experiments were conducted to compare the water/fat separate reconstruction, which separately reconstructs water and fat susceptibility maps based on the water/fat separation, with conventional QSM with body masking. The proposed method improved susceptibility estimation specifically in only the water tissue. The results of the human experiments were consistent with those of the numerical simulations. The lack of phase information outside the body contributed to susceptibility underestimation in conventional QSM. The developed method addressed susceptibility underestimation only in water tissue in body QSM.</p>