There are many studies devoted to conquer the strength–ductility trade‐off dilemma of polylactic acid (PLA) by flexible elastomer blending, like thermoplastic polyurethane (TPU), but little is known about the effects of the fused deposition modeling (FDM) process on the in situ morphology evolution of the elastomers. In this work, the effects of the three successive drawing processes in FDM on the morphology evolution of the dispersed TPU in the PLA matrix, and the toughening behavior of FDM‐printed PLA/microfibrillar‐TPU blends, are systematically studied. The results manifest that the average length of the TPU microfibrils can be turned precisely from 67.24 to 103.72 µm. The in situ microfibrillation process can remarkably improve the PLA crystallization capability and interfacial interaction. More interestingly, the inevitable decrease of impact strength of FDM‐printed part induced by the voids is compensated by the network‐like TPU microfibrils formed during the layer‐by‐layer printing. These inspiring findings suggest that the in situ fibrillation process can conquer the inherent weaknesses of both FDM process and PLA materials, providing facile and efficient method for fabricating high toughness PLA parts.