Euglena gracilis EOD-1, a microalgal strain, produces large quantities of paramylon, a class of polymers known as β-1,3-glucans and has been reported to function as a dietary fiber and to improve the metabolic syndrome including obesity. However, despite its importance, the morphometric analysis of paramylon has not been conducted so far. In this study, we attempted to observe the detailed three-dimensional structure of paramylon by focused ion beam/scanning electron microscopy (FIB/SEM). Paramylon samples were fixed and three-dimensional image reconstruction and segmentation of the image stack were created using computer software (Amira v6.0.1, FEI). The results indicated that the inside of paramylon particles (diameter: 5 µm, thickness: 3 µm) was comprised of a dense structure with no evidence of the presence of large pores and gaps, although a small 100 nm crack was observed. The specific surface area of paramylon particles measured by the Brunauer–Emmet–Teller (BET) method, was not as large as activated charcoal, but similar to those of plant starches, indicating that the cholesterol-lowering effect of paramylon cannot be simply attributed to its adsorption ability. The FIB/SEM method was found to be useful for elucidating the internal structure of small solid particles.