The complex environment of living organisms significantly challenges the selectivity of classic small-molecule fluorescent probes for bioimaging. Due to their predesigned topological structure and engineered internal pore surface, covalent organic frameworks (COFs) have the ability to filter out coexisting interference components and help to achieve accurate biosensing. Herein, we propose an effective interference-resistant strategy by creating a COF-based hybrid probe that combines the respective advantages of COFs and small-molecule probes. As a proof of concept, a two-photon fluorescent COF nanoprobe, namely TpASH-NPHS, is developed for targeting hydrogen sulfide (H2S) as a model analyte. TpASH-NPHS exhibits limited cytotoxicity, excellent photostability and long-term bioimaging capability. More importantly, compared with the small-molecule probe, TpASH-NPHS achieves accurate detection without the interference from intracellular enzymes. This allows us to monitor the levels of endogenous H2S in a mouse model of cirrhosis.