Abstract Higher education is the engine of knowledge-based economy in the country. Universities, the cradle of science and wealth of each country. Production of knowledge achieved with the thesis quality and functional. But today the reasons thesis of graduate without the use of libraries and faculty offices, soil again. The researcher tries to model the thinking process of the theory of constraints, bottlenecks in the way of this process stereotypically Graduate University in Yazd, around the time of spring and summer of 2015 to explore and investigate. In order to collect data, interviews with three panels of experts with knowledge of the agenda and Comprehensive study, the results to be deduced. The most important feature is undesirable, inappropriate choice of subject was unanimous, the basic problem, was elected documents. The poor quality of student input in this stage of the selection process on the one hand and on the other hand, The most important bottlenecks in the way the process was considered a master of Yazd University.