The invention provides a method of controlling building settlement caused by penetration of a jacked pipe through grout replacement. The existing method of controlling the settlement of a building penetrated by the jacked pipe generally focuses on prediction before the jacked pipe penetrates the building, drag reduction by injecting when the jacked pipe penetrates the building and repair by injecting when abnormal settlement occurs after the jacked pipe penetrates the building; the construction method of actively and directly controlling the settlement is absent. According to the technical scheme, the method is characterized in that after the jacked pipe penetrates from beneath the building, cement grout is slowly and evenly injected in from a discharge hole preformed in a jacked pipe segment; thixotropic slurry is pressed down by the cement grout, and finally is discharged out of a discharge hole below the jacked pipe segment; meanwhile, the slurry discharged from the discharge hole is observed; when the discharged slurry turns into the cement grout, injecting of the cement grout is stopped and grout replacement is complete. By replacing the slurry materials and utilizing the reasonable injecting process, the settlement of the building when the jacked pipe downwardly penetrates the building is reduced effectively.