Seed oil content is an important characteristic for the potential biofuel feedstock benzoin (Styrax tonkinensis). With the aim of further understanding benzoin lipid biosynthesis, the endosperm and embryo cell ultrastructures were acquired through transmission electron microscopy (TEM); the relative oil body area per cell (ROA) and oil body diameter (OBD) were then calculated by analyzing TEM images via computer software. The endosperm ROA peaked at 99 days after flowering (DAF) (79.04%), and the embryo ROA dynamic fitted the “S” curve. Significant linear relations (p < 0.01) were only observed between endosperm ROAs and the contents of whole-kernel crude lipid and fatty acids. The endosperm OBD (1.18–2.43 μm) was larger than that of embryo OBD (0.38–0.77 μm). M-shaped dynamics of acetyl coenzyme carboxylase (ACC) and diglyceride acyltransferase (DGAT) activities resembled the dynamic of endosperm OBD, as two peaks were observed at 78 and 113 DAF; the big oil body (≥1.8 μm) fraction in endosperm increased as kernel ACC and DGAT activities also increased, and vice-versa. Embryo OBD gradually increased, with the big oil body (≥0.5 μm) proportion increasing and the small oil body (<0.5 μm) proportion decreasing in general. Our results collectively suggested the distinct lipid accumulation patterns in the two benzoin kernel tissues, and revealed that the endosperm may determine the whole kernel oil biosynthetic process.