The internal quality assurance system of graduate student education is analyzed to propose the internal quality assurance architecture according to the process of inputting protection, training process protection, outputting protection. The internal quality assurance in line with the law of graduate student education which can effectively operate is established by ensuring the graduate student enrollment, constructing the tutors, improving the culture conditions, optimizing training, monitoring the quality of the master thesis, improving employability, constructing the internal evaluation system and so on. The standardized and scientific, systematic and institutionalized graduate student education is realized to innovating the graduate student education, realizing the graduate student education quality management and assurance.