This study employed a high-extrusion-rate Fused Deposition Modeling (HFDM) 3D printer, with the nozzle diameter enlarged from 0.4 mm to 1.0 mm. The increase in nozzle diameter (from 0.4 mm to 1.0 mm) significantly enhanced the volumetric deposition rate, thereby reducing the time required to print each layer and shortening the overall manufacturing cycle. In addition, the larger nozzle diameter increased the width and height of each printed bead, which shortened the required path length per layer, further improving printing efficiency. Short-carbon-fiber filled polyamide 12 (PA12-CF) is used as the test material. The three-point bending test samples are prepared with the HFDM system, where the effects of extrusion width and layer height, as printing parameters, on the flexural properties are investigated. Furthermore, the fiber orientation within the deposited beads is measured using optical microscopy and imaging process software ImageJ. Experimental results indicate that with an increased layer height and extrusion width, PA12-CF samples exhibit improved mechanical properties, where the bending strength and stiffness can be increased up to ~ 20%, and ~ 30%, respectively. The fiber orientation angle measurements indicate that with smaller values of layer height and extrusion width, the fibers tend to align more parallel to the material extrusion direction. As these printing parameters increased, the fibers tend to align more diversely to the transverse directions, which ultimately benefits the increment of the flexural resistance of the entire samples. Additionally, isothermal annealing process improves the bending strength and bending modulus of the samples by approximately 12% and 13%, respectively.