Lightweight and cost-effective polymer matrix composites (PMCs) with extraordinary mechanical performance will be a key to the next generation of diverse industrial applications such as aerospace, electric automobile, and biomedical devices. Limpet teeth made of mineral-polymer composites have been proved as nature’s strongest material due to the unique hierarchical architectures of mineral fiber alignment. Here, we present an approach to build limpet teeth inspired structural materials with precise control of geometric morphologies of microstructures by magnetic field-assisted 3D printing (MF-3DP). α-Iron (III) oxide-hydroxide nanoparticles (α-FeOOHs) are aligned by the magnetic field during 3D printing and aligned α-FeOOHs bundles are further grown to aligned goethite-based bundles (aGBs) by rapid thermal treatment after printing. The mechanical reinforcement of goethite-based fillers in PMCs can be modulated by adjusting the geometric morphology and alignment of mineral particles encapsulated inside the 3D printed PMCs. In order to identify the mechanical enhancement mechanism, physics-based modeling, simulation, and tests were conducted and the results further guided the design of bioinspired goethite-based PMCs. The correlation of the geometric morphology of self-assembled α-FeOOHs, curing characteristics of α-FeOOHs/polymer composite, and process parameters were identified to establish the optimal design of goethite-based PMCs. The 3D-printed PMCs with aGBs show promising mechanical reinforcement. This study opens intriguing perspectives for designing high strength 3D printed PMCs on the basis of bioinspired architectures with customized configurations.