By accounting for the external and internal force acting on the suspended magnetic nanoparticles and motion characteristics of the suspended magnetic nanoparticles in the magnetic fluids, the three-dimensional microstructure of magnetic fluids is investigated by means of the molecular dynamics simulation method. The distribution of suspended magnetic nanoparticles and microstructure of the magnetic fluid are simulated in both absence and presence of an external magnetic field. The effects of the nanoparticles volume fraction, the dipole-dipole interaction potential and the particle-field interaction potential on the microstructures of the magnetic fluids are discussed. The main results obtained here are summarized as follows. The suspended magnetic nanoparticles tend to aggregate and make the irregular distribution structure in the absence of an external magnetic field. When the magnetic fluid is exposed to a magnetic field, the magnetic nanoparticles suspended in the carrier fluid tend to remain chained-alignment in the direction of the external magnetic field. The tendency of chain-alignment morphology of the suspended magnetic nanoparticles is enhanced with the nanoparticles volume fraction, the dipole-dipole interaction potential and the particle-field interaction potential.