Heat shock protein 90 (HSP90) is a powerful molecular chaperone responsible for the stability and integrity of various client proteins, including various transcription factors, kinases, and steroid hormone proteins, among others. Overexpression of HSP90 is closely related to cancer, immune diseases, and neurodegenerative diseases. However, there are few effective fluorescent probes for HSP90. Therefore, we synthesized a near-infrared fluorescent probe YQHSI-MPA-1 targeting HSP90. The probe was later structurally modified to improve the targeting specificity and accuracy in vivo as YQHSI-MPA-2. Furthermore, the application values of YQHSI-MPA-2 in situ CRC, AOM-DSS-induced CRC, and various metastasis models were evaluated. The results showed that YQHSI-MPA-2 had excellent specificity and high tumor contrast. In conclusion, YQHSI-MPA-2 is an ideal tool for tumor detection and surgical navigation.