This study examined the effect of cancellous bone microstructure on stress distribution within a premolar tooth and a dental implant against mastication force by the micro-finite element method (FEM). The mandibular specimen including a premolar was obtained from a cadaver and scanned with micro-CT to obtain CT images. FE models were reconstructed from CT images at mid-sagittal plane of the tooth. Six models were generated and analyzed for different structure and density in cancellous bone. Stress distributions for each implant (or tooth) and the surrounding bone were compared. The study indicated that the microstructure of cancellous bone should be considered in finite element analysis to produce reasonable results and thus implant systems with high success rate.