As one of the indispensable actuating components in micro-systems, the shafted microgear is in great production demand. Microforming is a manufacturing process to produce microgears to meet the needs. Due to the small geometrical size, there are uncertain process performance and product quality issues in this production process. In this study, the shafted microgears were fabricated in two different scaling factors with four grain sizes using a progressively extrusion-blanking method. To explore the unknown of the process, grain-based modeling was proposed and employed to simulate the entire forming process. The results show that when the grains are large, the anisotropy of single grains has an obvious size effect on the forming behavior and process performance, the produced geometries and surface quality are worsened, and the deformation load is decreased. Five deformation zones were identified in the microstructures with different hardness and distributions of stress and strain. The simulation by using the proposed model successfully predicted the formation of zones and revealed the inhomogeneous deformation in the forming process. The undesirable geometries of microgears including material unfilling, burr and inclination were observed on the shaft and teeth of gear, and the inclination size is increased obviously with grain size. To avoid the formation of inclination and material unfilling, the punch was redesigned, and a die insert was added to constraint the bottom surface of the gear teeth. The new products had then the better forming quality.