Fecal impaction is a gastrointestinal problem that occurs in all age groups. Traditional therapy with drugs or surgery may result in serious complications for patients. Softening hard stool in vitro is realized with swaying Fe3O4 nanoparticle (NP) aggregates controlled by an oscillating magnetic field generated using a combination of electromagnetic coils and permanent magnets. The operation mechanism of the combined oscillating magnetic field is analyzed, experiments on NP manipulation by the magnetic field are conducted, and the morphology and sway motion characteristics of the aggregates are observed under various experimental parameter settings. Experimental results show that such NP aggregates manipulated by oscillating magnetic fields can be applied to soften stool in the rectum for fecal impaction treatment. In addition, diagnosis and sensing of constipation induced by obstruction in the gastrointestinal tract can be executed by the same approach in the future.