Muhammadiyah Boarding School Yogyakarta is an Islamic education institution whose job is to foster santri regarding religion which includes the santri characters building. Things that must be considered in the process of character building between santri and the supervisor are emphasizing the discipline of santri and educating them to be honest, trustworthy, intelligent, and responsible. One form of communication carried out by santri with their supervisors is interpersonal communication that requires closeness between them so that the message delivered can be achieved perfectly. This study aims to find out the processes that occur in the interpersonal communication of santri with supervisors in character building at the Muhammadiyah Boarding School in Yogyakarta and explain it’s supporting and inhibiting factors that occur. This research uses qualitative descriptive approach. Data collection techniques carried out include observations, interviews, and documentation. The results of this study indicate that the interpersonal communication process between santri and the supervisor in character building uses a psychological approach. The factor that supports interpersonal communication is the use of the language of supervisor for santri which is easy to understand. The inhibiting factor found is the lack of self-confidence of students to carry out interpersonal communication with their supervisors.