Background: Previous studies have shown that a single Coma-Recovery Scale-Revision (CRS-R) assessment can identify high misdiagnosis rate for a clinical consensus. The aim of this study was to investigate the misdiagnosis rate of clinical consensus compared to repeated behavior scale assessments in patients with prolonged disorders of consciousness (DOC). Methods: Patients with prolonged DOC during hospitalization were screened by clinicians, and the clinicians formed a clinical consensus diagnosis. Trained professionals also used the CRS-R to evaluate the consciousness levels of the enrolled patients for repeated times (≥5 times) within a week. After the repeated evaluation results, the enrolled patients with prolonged DOC were divided into unresponsive wakefulness syndrome (UWS), minimally conscious state (MCS), and emergence from MCS (EMCS). Furthermore, the relationship between the results of the CRS-R and the clinical consensus were analyzed. Results: In this study, 137 patients with a clinical consensus of prolonged DOC were enrolled. After the single CRS-R behavior evaluation, it was found that the misdiagnosis rate of clinical MCS was 24.7%, while the repeated CRS-R evaluation results showed that the misdiagnosis rate of clinical MCS was 38.2%. A total of 16.7% of EMCS cases were misdiagnosed as MCS, and 1.1% of EMCS cases were misdiagnosed as UWS. Conclusions: The current clinical consensus of the misdiagnosis rate is still relatively high. Therefore, clinicians should be aware of the importance of the bedside CRS-R behavior assessment and should apply the CRS-R tool to daily procedures.