Abstract Room temperature phosphorescence (RTP) materials are characterized with emission after removing the excitation source. Such long‐lived emission feature possesses great potential in biological fluorescence imaging because it enables a way regarding temporal dimension for separating the interference of autofluorescence and common noises typically encountered in conventional fluorescence imaging. Herein, we constructed a new type of mesoporous silica nanoparticles (MSNs)‐based composite nanoparticles (NPs) with dual‐color long‐lived emission, namely millisecond‐level green phosphorescence and sub‐millisecond‐level delayed red fluorescence by encapsulating a typical RTP dye and Rhodamine dye in the cavities of the MSNs with the former acting as energy donor (D) while the latter as acceptor (A). Benefiting from the close D‐A proximity, energy match between the donor and the acceptor and the optimized D/A ratio in the composite NPs, efficient triplet‐to‐singlet Förster resonance energy transfer (TS‐FRET) in the NPs occurred upon exciting the donor, which enabled dual‐color long‐lived emission. The preliminary results of dual‐color correlation imaging of live cells based on such emission feature unequivocally verified the unique ability of such NPs for distinguishing the false positive generated by common emitters with single‐color emission feature.