The aim of this study was to detect the determinations of the 3D cell deformations of pine wood (Pinus sylvestris L.) in micro-scale(mu m) under mechanical compression loading. The 20 x 20 x 50 mm 3 sized wood specimens were tested under compressive pressure load through 35-40 MPa parallel to the grain orientations. The pressure applied samples were divided into three parts, then processed to form smaller cubic pieces and this pieces stained with gold liquid in order to get scanning electron microscopy images (12 x 12 x 12 mm(3) parts). The deformed cells were photographed in 3D-plane with magnification of (100 x), (1500 x) and in the range of 3.0-5.0 kV light voltage under the scanning electron microscope. Unloaded and loaded pine wood specimens were visualized and photographed to observe and examine the contraction or expansion of the cell walls comparatively. Based on the experimentally obtained microstructural permanent deformations of the cell structures, a numerical model had been proposed to explain the complex behaviour of cell structures under compression loading. Using the finite element method and ANSYS code, the permanent deformation ratios of three different pinewood cell models were simulated for 35-40 MPa loading to explain the overall stiffness and strength of the pinewood cells. In this way, by considering the results obtained from scanning electron microscopy measurements and related finite element analysis solutions, permanent deformation of honeycomb type pinewood cells was examined in detail.