The tight organization of major wood cell wall polymers limits the swellability, solubility and reactivity of cellulose fibers during the production of regenerated textile fibers, nanocellulose, bioethanol, and many other value-added products. However, the ultrastructural assembly of cellulose elementary fibrils (EF) and matrix materials in one of the outer layers, i.e. S1-2 transition layer of wood cell wall, is far from being understood. Here, single-axis electron tomography on ultrathin spruce sections was applied to observe the three-dimensional (3D) structure of the S1-2 layer. The nanoscale geometries of the EFs were further quantitatively modeled through mathematical fitting of the tomographic subvolumes by suitable parametric space curves. The results showed that crisscross, bundled and parallel EF organizations are all present in this layer; the former two exhibit a denser structure. Several quantitative measures such as distances and angles were obtained for the analyzed structures. The result obtained in this study suggests that the S1-2 transition layer differs in structure than the principal cell wall layers. The structural differences and its possible role in wood cell wall have been discussed. These results will enhance our understanding of the swellability, accessibility and solubility of woody biomass for its conversion into the aforementioned value-added products.