Purpose: Soils located in magnesite mining areas in Northeast China are covered with a hard white crust that increases soil pH and affects ecological functions, reducing water penetration rate in soil. This study aimed to investigate the effects of citric acid (CA) and polyacrylamide (PAM) on the inhibition of crust formation.Methods: Light-burned magnesia (LBM) obtained from a magnesite calcination factory in Haicheng were mixed with soil and filled into the upper layer of the soil column. Four treatments were denoted the control, M, M-PAM, and M-CA and subjected to simulated rainfall in a leaching experiment. The microstructure and phase composition of the crust covering on the upper layer of the columns were determined using various methods.Results: Soil infiltration rate (IR) decreased from 0.48 to 0.17 mm·min−1 when crust formed on the soil surface. Soil IR increased to 0.56 mm·min−1 after adding PAM to the soil, while the application of CA returned a maximum IR of 0.71 mm·min−1. Pores and cracks on soil surfaces treated with CA were larger than those treated with PAM. PAM prevented soil particles from reuniting into large aggregates and favored water osmosis. CA can be triple protonated and react with the main components of the crust. In summary, CA was an effective modifier for treating the crust compared to PAM.Conclusions: The CA treatment returned a 0.15 mm·min−1 higher soil IR and lower soil pH than the PAM treatment. CA is strongly recommended for controlling crust formation in magnesium soils because of its greater potential to react with Mg in the crust.