The aim of this study was to investigate how the alteration of the angulation of osteotome at pterygomaxillary junction affects lateral pterygoid plate, maxillary tuberosity, palatal surface of maxilla, palatine bone and body of sphenoid bone. Following reconstruction of 3D modelling of maxilla, Osteotomes' tip was angulated 45 and 90 to sagittal plane to simulate pterygomaxillary osteotomy. Finite element analyses (FEA) was performed and Von Misses stress distributions were analyzed for two different angulations. Independent sample t test was used to compare differences between 45 and 90 angulations. Von Misses stress values on lateral pterygoid plate were higher in 45 angulation (0.71 ± 0.21 MPa) than 90 angulation (0.54 ± 0.28 MPa). This difference was statistically significant (P < 0.01). Placement of osteotome's tip with 90 angulation had higher stress value than 45 angulation on maxillary tuberosity region. However; difference wasn't significant (P = 0.44). Stress values on body of sphenoid bone were 0.45 ± 0.17MPa for the case of 90 angulation and 0.19 ± 0.09MPa for 45 angulation. Difference between these values were statistically significant (P < 0.01). Possible risk of unfavourable lateral pterygoid plate fracture and complications related with body of sphenoid bone during pterygomaxillary osteotomy was remarkably increased in case of narrow angulation (45). Keeping osteotome at right angle with sagittal plane may avoid these complications.