Bowen’s disease (BD) is a relatively rare early-stage squamous cell carcinoma in situ, most commonly affecting the middle-aged and elderly, and occurring on the skin or mucous membranes of various parts of the body. Its onset is concealed, the course of the disease is chronic, and some patients are accompanied by malignant tumors outside the skin, so it is necessary to diagnose and evaluate the disease in its early stage. This study aims to investigate the application of reflectance confocal microscopy (RCM) in diagnosing Bowen’s disease. We performed RCM imaging on the lesion site of 113 patients initially diagnosed with Bowen’s disease in clinic, of which 92 patients underwent skin biopsy for histological diagnosis. A retrospective analysis of the RCM result as well as the histological examination revealed that after analyzing RCM images, 69 out of 113 patients were diagnosed with Bowen’s disease; out of 92 biopsy lesions, 61 were Bowen’s disease, of which 54 were consistent with RCM diagnosis. Among 59 cases diagnosed with Bowen’s disease by RCM, 54 cases were consistent with histological diagnosis. Afterwards, we analyzed the RCM characteristics in patients with Bowen’s disease verified by biopsy, and compared the RCM images of two different lesions, Classic Bowen’s Disease (CBD) and Pigmented Bowen’s Disease (PBD), and further summarized the key points of Bowen’s disease under RCM. Finally, we focused on the differential characteristics between Bowen’s disease and other skin diseases under RCM. It is found that RCM is of great value in diagnosing Bowen’s disease.