Laser powder bed fusion (L-PBF) is an additive manufacturing technology widely applied to the manufacture of metallic parts. The L-PBF processed aluminum-silicon (Al–Si) cast-type alloy components exhibit an anisotropic tensile ductility. In this study, we investigated the influence of heat treatments on the microstructural features of an Al–12%Si binary alloy fabricated via L-PBF and the associated inhomogeneous deformation of its melt-pool structure, which contributes to the resulting anisotropic tensile ductility. The mechanical inhomogeneity of the melt-pool structure and the change induced by annealing at various temperatures (300 and 530 °C) were characterized using microscale digital-image correlation analyses of scanning electron microscopy images obtained in situ during tensile deformation and nanoindentation hardness mapping. In the specimen fabricated via L-PBF, the high strain was concentrated at the locally coarsened microstructure (the soft region) along the boundaries of the melt pools rather than at the refined solidification microstructure (the hard region) within the melt pools. The localized strain varied depending on the geometrical relation between the orientation of the melt-pool boundary and the tensile direction, thus contributing to the anisotropic tensile ductility. This tendency appeared less pronounced in the specimen annealed at 300 °C, which exhibited a slightly homogenized melt-pool structure. The reduced strain localization is associated with a reduced difference in local strength between the melt-pool boundary (soft region) and the melt-pool interior (hard region). The slight homogenization of the melt-pool structure emphasized the effect of grain morphologies in the α-Al matrix on the inhomogeneous deformation within melt pools. In the specimen annealed at 530 °C, which exhibited a homogenized α-Al/Si two-phase microstructure, the uniformly distributed Si phase would be responsible for the homogenous deformation, resulting in an isotropic tensile ductility. This study advances our understanding of the correlation between the melt-pool structure and the deformation behavior of Al–Si alloys processed using L-PBF, which provides new insights for controlling the ductility by post-processing.