X-ray micro-tomography (µCT) scans and a coupled multiphase model based on computational fluid dynamics (CFD) and discrete element method (DEM) are used to investigate the fibre flow inside the printer nozzle during 3D printing of short fibre reinforced thermoplastic composites by fused filament fabrication (FFF). Short carbon fibre T300 reinforced nylon-6 composite is selected as the printing material. X-ray CT is performed on the raw filament, in-nozzle melted filament, extruded printing bead and on-bed printing bead to trace the through-process evolution of fibres and voids for the specific nozzle used therein. Qualitative visualisation of voids fraction and fibre orientation, length and fraction, as well as quantitative analysis are carried out using image processing techniques. The results show that the orientation and volume fraction of fibres vary with different internal geometry of the nozzle and fibre misalignment occurs in the on-bed printing bead because of the relative motion between the nozzle and the print bed disturbs the flow field. Also, the fibre length decreases slightly during the printing process due to the collision between fibre and nozzle wall when the melted materials pass the nozzle. Most voids are generated when the melted filament is extruded from the nozzle, and porosity decreases in the on-bed printing bead. In addition, a coupled CFD-DEM is developed, in which the collisions between fibres are considered naturally in DEM by using the Hertz-Mindlin contact law. Once validated against X-ray microtomography (uCT) experimental results, a parametric study is performed using the CFD-DEM model to investigate various fibre lengths, fibre volume fraction and resin viscosity. It shows that the nozzle clogging tends to occur when the fibre length and/or the fibre volume fraction are increased. The use of a polymer matrix with lower viscosity can be effective to eliminate the clogging issue when printing composites with relatively short fibres. The fibre length is dominating when long fibres are used and the clogging is largely independent of the viscosity of the polymer matrix. Finally, a potential solution of using a cone sleeve insert located above the shrinking region to address the nozzle clogging issue is proposed and numerically assessed.