Characterizing of physical and mechanical properties of rocks are very important in design stage of rock engineering works. Particularly mechanical properties of rocks which show the relationship between applied different stress conditions and corresponding deformability and failure are so important. Rock fracture toughness shows the strength of rock against crack initiation and propagation. Several issues such as intrinsic, environmental and laboratory aspects, may affect the rock fracture toughness. Among the different environmental phenomena, chemical alteration which changes the mineralogical composition of rocks has a great influence on resistance of rocks against crack initiation and propagation. This issue didot address in the literature and is the main objective of this study. Using numerical Discrete Element Method approach, generation of real mineralogical patterns of rock and also modeling of crack propagation with considering mechanical interaction between different mineral compositions, is possible. Two altered/unaltered quartz diorite rock samples, from Godar Siavash(GS) quarry stone mine in Natanz were selected as basement in this study. Percentage and grain distribution of mineral composition were recognized with microscopic study on thin sections. Physical and mechanical properties of quartz diorite sample were also measured in laboratory. Then several realizations of grain patterns were generated by Voronoi Elements and Universal Distinct Element Code (UDEC) and micromechanical properties of numerical modeling were approximated using back-calculation techniques through numerical calibrations. In order to specifying of changes on fracture toughness in altered and unaltered samples, a series of numerical modellings by Hollow Centre Cracked Disc (HCCD) were conducted. The results show that the calculated fracture toughness in altered samples are very small compared to the unaltered models, it also showed that the distribution of altered minerals in models particularly in the vicinity of pre-existing crack is violated the crack propagation path.