The COVID-19 pandemic has emphasized the need for non-contact medical robots to alleviate the heavy workload and emotional stress experienced by healthcare professionals while preventing infection. In response, we propose a non-contact robotic diagnostic system for otolaryngology clinics, utilizing a digital twin model for initial design optimization. The system employs a master-slave robot architecture, with the slave robot comprising a flexible endoscope manipulation robot and a parallel robot arm for controlling additional medical instruments. The novel 4 degrees of freedom (DOF) control mechanism enables the single robotic arm to handle the endoscope, facilitating the process compared to the traditional two-handed approach. Phantom experiments were conducted to evaluate the effectiveness of the proposed flexible endoscope manipulation system in terms of diagnosis completion time, NASA task load index (NASA-TLX), and subjective risk score. The results demonstrate the system’s usability and its potential to alternate conventional diagnosis.