Clinical studies have shown that fluorescent molecular imaging technology is extensively utilized in intraoperative navigation, tumor boundary recognition, in vivo microscopic pathology diagnosis, etc. However, identification of tumor boundaries through in vivo biopsy remains a challenging task owing to the slight discrepancy between tumor tissue and surrounding normal tissue in optical imaging. To better distinguish tumor tissue and observe histopathology in clinical examination, a dual-mode switching endomicroscopic system was proposed in this paper, which consisted of wide-field imaging for surgical navigation and microscopic imaging for performing tumor boundary recognition. The system employed sodium fluorescein as a fluorescent molecular probe and an in-house developed blue LED with high-brightness as an excitation source. Fast switching between two modes was an advantageous design for clinical surgery to effectively determine benign and malignant tumors during in vivo microscopic pathology analysis. This paper examined the feasibility of the dual-mode imaging system for mouse liver inspection in vivo. The experimental results show that dual-mode imaging can identify tissue color and boundary features with a resolution of 4.4 μm. The system can meet the clinical demands of real-time surgical navigation and microscopic pathological diagnosis of in vivo tumors.