Ferrofluid (FF) has attracted more and more attention due to its tunable rheological properties, in which the microstructure under a magnetic field plays an important role in these properties. In this study, an innovative coarse-grained (CG) model of FF is presented for the first time to capture the microstructure evolution of FF at the nanoscale. The potential functions of carrier liquid for FF CG models are obtained by the iterative Boltzmann inversion (IBI) method, and the CG nonbonded interaction between the magnetic particles (MPs) is obtained via the strain energy conservation. Then, CG molecular dynamics (CGMD) simulations are used to study the microstructure evolutions of FF under different magnetic fields. Notably, we demonstrate the existence of a carrier liquid adsorption layer on the MPs surface, and its thickness is calculated. The staggered arrangement style of MPs in the chains is also revealed by the CGMD method. The present FF CG model has fully considered the carrier liquid molecular structure and interaction with the MPs, and the CGMD is used to solve the problem that classical molecular dynamics cannot simulate the microstructure of FF, making the simulation results more in line with the actual situation.