The AlCoCrFeNi2.1 eutectic high-entropy alloy (EHEA), as a kind of in-situ composite materials, have achieved good match of strength and plasticity due to its typical eutectic lamella structures. Although many previous studies have investigated the indentation behaviors of the AlCoCrFeNi2.1 EHEA, there are still some controversies about the hardness characteristic of different crystal structures, requiring further clarification. Accordingly, in this study, nanoindentation tests were conducted to investigate the indentation behaviors of different crystal structures (primary L1(2) phase, primary B2 phase, and the eutectic phase region). The residual indentation and the crystallographic orientations were characterized by the laser scanning confocal microscope, scanning electron microscope, and electron backscatter diffraction. The hardness in different crystal structures were comparatively analyzed and the material deformation mechanisms were discussed correspondingly. The statistic results showed that the eutectic phase region had the lowest hardness, and primary B2 phase had the highest hardness. Furthermore, the slip lines in the primary L12 phase were evenly distributed near the residual indentation, but the slip lines in the eutectic phase region were concentrated near the phase boundaries. These findings are expected to deepen the understanding of the microscale deformation behaviors of EHEAs.