The selection of optimal process parameters has a decisive effect on the quality of 3D printing. In this work, the numerical and experimental methods were employed to investigate the FDM printing deposition process of PLA/GNPs nanocomposite. The effect of process parameters on cross-sectional morphology and dimension of the deposited filament, as well as the mechanical property of the FDM printed specimens were studied. The extrusion and the deposition process of the molten PLA/GNPs nanocomposite was simulated as a fluid flow by the paradigm of CFD, the effects of printing temperature and shear rate on thermal-physical properties, such as viscosity and surface tension, were considered in models. Under the assumptions of non-Newtonian fluid and creep laminar flow, the deposition flow was controlled by two key parameters: the nozzle temperature and the nozzle velocity. The numerical model was verified by experiments from four aspects of thickness, width, area, and compactness of the deposited PLA/GNPs nanocomposite filament cross-section. Both the numerical simulation and experiment results show that with the increase of nozzle temperature and nozzle velocity, the thickness, area, and compactness of the deposited filament decreases. While the width of deposited filament increased with the increase of nozzle temperature and decrease of nozzle velocity. The decrease in thickness and the increase in width caused by the change of process parameters reached 10.5% and 24.7%, respectively. The tensile strength of the printed PLA/GNPs specimen was about 61.8 MPa under the higher nozzle temperatures and velocity condition, an improvement of 18.6% compared to specimen with the tensile strength of 52.1 MPa under the lower nozzle temperatures and velocity condition. In addition, the experimental results indicated that under the low nozzle velocity and nozzle temperature condition, dimensional standard deviation of the printed specimens decreased by 52.2%, 62.7%, and 68.3% in X, Y, and Z direction, respectively.