The lecturer is the most important factor for success in achieving the educational goals. Hence, paying attention to effective teaching leads to achieving the educational goals and the improvement of learning process. The goal of this study was to prioritization and to determine the relationship between factors affecting the effective teaching by lecturer in graduate student’s perspective. In this analytical study, all Graduate students of Allied Medicine School in Tehran University of Medical Sciences (105 students) in the second semester in 2012-2013 were selected. Moreover, a valid and reliable questionnaire used for data collection consisted of nine factors influencing the effectiveness of teaching. Data was analyzed using graph theory and Matlab software. Factors of mastery of the subject, providing new and updated content, simply and fluently state, and clearly transfer the contents certainly influence and impact on the effectiveness of teaching. In addition, two factors including mastery of the subject and evaluation of students in each session, mid-term and end of term with coordinates of (1.14 and 1.14) and (1 and -1) were identified as first and last priority respectively. The results showed that the most important factor was mastery to training content. Therefore, considering the importance of improving the quality of education as well as in order to increase communication skills between lecturer and student, and acquaintance to teaching methods, it is also proposed the appropriate targeted workshops and training courses take place.