Lysosome of phagocyte is the main site of hypochlorous acid (HClO) production, and HClO can be employed as the biomarker for the diagnosis and treatment evaluation of arthritis. In recent years, developing fluorescent probes for lysosomal HClO has attracted considerable attention, but most of them still have some defects, such as autofluorescence, phototoxicity and photobleaching because of their excitation and emission located in short-wavelength region. Due to the advantages of two-photon fluorescent probes with near-infrared emissions, a lysosome-targetable two-photon fluorescent probe (Lyso-TP-HClO) with a near-infrared emission was reported in this paper. Lyso-TP-HClO has a high selectivity and a high sensitivity to HClO in the linear range (10.0 × 10−8 to 5.0 × 10−6 M), with a detection limit of 3.0 × 10−8 M. Due to the two-photon excited near-infrared emission, Lyso-TP-HClO has excellent imaging performances, such as small autofluorescence, excellent photostability, and large imaging depth. Furthermore, Lyso-TP-HClO was successfully employed for visualizing lysosomal HClO in bacteria-infected cells. At last, we have successfully used Lyso-TP-HClO to image the arthritis and evaluate the treatment of arthritis in mice. All the results confirm that Lyso-TP-HClO is a useful chemical tool for imaging of lysosomal HClO, the diagnosis of arthritis, and treatment evaluation of arthritis.